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ChangeLog
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CHANGES
=======
* add disease examples
* add allele set
* add validator and example data
* Updating generated outputs
* Change curie to unique\_id
* Updating generated outputs
* Remove identifier flag
* Replace curie with unique\_id on DiseaseAnnotation
* Updating generated outputs
* Add gene\_type slot linking gene to SOTerm
* Updating generated outputs
* Fix typo
* Remove abbreviation definition as moved to core
* SCRUM-879 vocabulary changes
* Updating generated outputs
* SCRUM-963 Add letter code abbreviations of ECO terms
v1.0.0
------
* Updating generated outputs
* Made MA ontology term a type of anatomical term
* Updating generated outputs
* Made 'paper\_handle' slot plural 'paper\_handles'
* PaperHandle class, paper\_handle slot, other edits
* Updating generated outputs
* Update molecule
* Updating generated outputs
* Clean up to disease and phenotype annotation yaml
* Updating generated outputs
* Initial use of inlining to create nested JSON schema
* Updating generated outputs
* Removed phenotype relation enum references
* Updated slot descriptions, added new slots and classes for phenotype and disease annotations
* Updating generated outputs
* Update allianceModel.yaml with controlledVocabulary import
* Removed unnecessary dash before 'definition' slot usage in ontologyTerm.yaml
* Updated vocabulary additions
* added controlled vocabulary yaml
* Updating generated outputs
* Add 'AuditedObject' mixin to Molecule class
* Updating generated outputs
* Update ExperimentalCondition slot\_usage ranges
* Updating generated outputs
* Define ConditionRelation class and add relevant slots
* Remove obsolete 'Disease' class
* Updating generated outputs
* Updating generated outputs
* Initial commit of schema for WB molecules
* Add descriptions and tidy up
* Updating generated outputs
* add more targets to store
* add makefile for javagen
* add java gene
* Updating generated outputs
* remove typo before id
* Inherit slots from parent DiseaseAnnotation class
* SCRUM-569 Disease annotation updates
* Updating generated outputs
* add gen-java
* add gen-java fix typo
* Added ExperimentalConditionOntologyTerm class
* Made "ECOTerm" range for "evidence\_code" slot
* fix typo
* add small changes to potentially restrict what goes in the modifier fields
* fixing class slots per review
* SCRUM-248 Update to required fields
* regenerate docs, etc
* fixing tests
* fixing tests
* fixing tests
* fixing tests
* fixing tests
* add several subclasses
* refactor disease annotation to be a superclass
* Added prefix stanza to the antibody schema yaml
* Set theme jekyll-theme-cayman
* Update phenotypeAndDiseaseAnnotation.yaml
* Change affected\_genes to affected\_entities
* Remove feature\_type slot
* Create MolecularMutation class
* Add details to embryonic\_cell\_lines slot
* Replace comments with notes tag
* Remove curie slot from CrossReference class
* Updating generated outputs
* fixing tests
* Updates to phenotypeAndDiseaseAnnotation.yaml
* Updating generated outputs
* Removed fields that exist in the is\_a class
* Updating generated outputs
* Removed the One to One relationship as no other classes use this class
* Removed redundant slots as these were on the parent classes
* Updating generated outputs
* Update main.yaml
* Updating generated outputs
* fix reference
* remove reference id
* remove docs
* fix refernee
* Updating generated outputs
* remove docs
* remove doc, add has\_allele
* Updating generated outputs
* fix figure
* edit workflow so it runs on a test branch
* fixing redundant names of slots and classes
* Updating generated outputs
* added docs ignores
* removed docs/
* Updating generated outputs
* Add docs/ to .gitignore
* Updating generated outputs
* Updating generated outputs
* fixing conflicts
* Updating generated outputs
* fixing Makefiel
* remove sqlalchemy for now
* add test.yaml
* Updating generated outputs
* Updating generated outputs
* Automatically generated requirements.txt and requirements-dev.txt
* fixing test
* fixing tests
* fixing tests
* fix circular crossReference
* remove double quotes
* fixing antibody
* fix linkml-model
* fix linkml-model error
* adding linkmk-model
* test actions
* removing redundant imports
* Create VariantConsequence parent class
* Remove duplicate variation slots
* Remove non-required slots as discussed in Allele WG
* Automatically generated requirements.txt and requirements-dev.txt
* remove test for now
* remove test for now
* flag other anatomy terms
* minor tidying
* remove redundant condition modeling
* add Figure and ImagePane
* fix range on orthology
* added ontologyterm ranges
* added ontologyterm ranges
* added ontologyterm ranges
* add gene synopsis descriptions
* ortho association classes
* externalDatabaseLink
* adding external id xref tables
* 1st draft xprn, image
* remove entity is a relation
* remove entity is a relation
* remove entity is a relation
* minimal changes required to get "make install all" working
* First submission of phentoypeAndDiseaseAnnotation.yaml to agr\_curation\_schema
* First submission of geneInteraction.yaml to agr-curation-schema
* orthology
* add construct relation, ontology term
* add AntibodyGene association
* update
* add Antibody
* fix tests
* remove the top level requirements from Pipfile
* rm env.lock
* adding linkml upstream
* adding linkml upstream
* adding linkml upstream
* adding linkml upstream
* adding linkml upstream
* messing with poetry
* messing with poetry
* messing with poetry
* try out different version of linkml
* try out different version of linkml
* fix pip
* update Pipfile to include linkml
* update Pipfile to include linkml
* fix dependency
* try adding linkml to the Pipfile
* try commiting make-venv
* try touching dir before install
* try touching dir before install
* try touching dir before install
* try touching dir before install
* remove duplicate target/ from gitignore
* alliance-model to allianceModel, fix docs and agr\_curation\_schema in .gitignore, remove test artifacts
* made GenomicEntity the base class for testing
* fix up config from linkml-config-model to agr\_curation\_schema config
* remove make-venv directory
* remove stray images directory
* Initial generation run
* update git ignore
* add workflows
* migrate currently checked in code to new repository
* Initial commit