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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.enanomapper.net/onto/external/msio-slim.owl#"
xml:base="http://purl.enanomapper.net/onto/external/msio-slim.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:pav="http://purl.org/pav/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.enanomapper.net/onto/external/msio-slim.owl">
<protege:defaultLanguage xml:lang="en">en</protege:defaultLanguage>
<obo:IAO_0000112 xml:lang="en">http://nmrml.org/examples/</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level.
This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.</obo:IAO_0000116>
<obo:IAO_0000116>BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science.</obo:IAO_0000116>
<obo:IAO_0000116>BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms.</obo:IAO_0000116>
<obo:IAO_0000232 xml:lang="en">In case we like to be able to convert this owl CV back into the obo format, we should only use DL/owl constructs that are supported by obo. Hence, editors of this CV should take care not to use any higher descriptrion logics semantics, i.e. cardinality restrictions or defined terms using constructors. We should start to build the taxonomic backbone first and later connect the main axis via relations.
If we want to use restrictions, we should only use existential quantifiers as the OBO format does not support universal quantification.
List of terms required by current XSD (August 2013): these were bookmarked in CV (annotation property) and are visible in the new nmrTab:
CVTerm occurrences:
buffer-->buffer
solvent-->solvent
concentration standard type-->calibration compound , what is chemical shift reference ? What calibration_reference_shift under calibration compound ?
concentration standard name we here see a use-mention problem arising for the CV. The xsd should probably change here to avoid this.
encoding method (Quadrature detection method) is this the same as encoding method ?
sample container-->NMR_sample_holder
(spectrum) y axis type-->coordinate system descriptor
post acquisition solvent suppression method Two usages in xsd, but with differrent type ? -->solvent suppression method
calibration compound Two usages in xsd, but with differrent type ?-->calibration compound
data transformation method-->data transformation method
(spectral) projection method-->projection method
spectral denoising method-->spectral denoising method
window function method-->window function method
baseline correction method-->baseline correction
sample type-->NMR sample
CVParam occurrences:
file content-->data file content
software type-->software
source file type-->data file attribute (needs refactoring)
instrument configuration type-->instrument configuration
processing method type-->data processing method
CVParamType occurrences:
chemical shift standard-->chemical shift standard
solvent suppression method-->solvent suppression method
encoding scheme (Quadrature detection method)-->encoding method
window function parameter-->window function parameter
CVParamWithUnitType occurrences:
CVParamWithUnitType is currently not used in the xsd and dangling ! I assume ValueWithUnitType substitutes it ?
UserParamType occurrences:
No CV terms needed
ValueWithUnitType occurrences:
These will have to be used from the Unit ontology.</obo:IAO_0000232>
<dc:contributor xml:lang="en">Alejandra Gonzalez-Beltran</dc:contributor>
<dc:contributor xml:lang="en">Andrea Porzel</dc:contributor>
<dc:contributor xml:lang="en">Andrew Lane</dc:contributor>
<dc:contributor xml:lang="en">Annick Moing</dc:contributor>
<dc:contributor xml:lang="en">Catherine Deborde</dc:contributor>
<dc:contributor xml:lang="en">Chris Taylor</dc:contributor>
<dc:contributor xml:lang="en">Daniel Jacob</dc:contributor>
<dc:contributor xml:lang="en">Daniel Schober</dc:contributor>
<dc:contributor xml:lang="en">David Wishart</dc:contributor>
<dc:contributor xml:lang="en">Dennis Rubtsov</dc:contributor>
<dc:contributor xml:lang="en">Helen Jenkins</dc:contributor>
<dc:contributor xml:lang="en">Hunter Moseley</dc:contributor>
<dc:contributor xml:lang="en">Irena Spasic</dc:contributor>
<dc:contributor xml:lang="en">Joseph Cruz</dc:contributor>
<dc:contributor xml:lang="en">Larissa Soldatova</dc:contributor>
<dc:contributor xml:lang="en">Marta Cascante</dc:contributor>
<dc:contributor xml:lang="en">Michael Wilson</dc:contributor>
<dc:contributor xml:lang="en">Pedro Ramon de Atauri Carulla</dc:contributor>
<dc:contributor xml:lang="en">Philippe Rocca-Serra</dc:contributor>
<dc:contributor xml:lang="en">Reza Salek</dc:contributor>
<dc:contributor xml:lang="en">Silvia Marin</dc:contributor>
<dc:contributor xml:lang="en">Since this is a prolonged effort spanning a larger time period, there naturally were many people involved in the creation over the years and during different times.
People involved in the term creation from ID >1400000 :
This part of the NMR ontology was originally developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net):
Dennis Rubtsov (Un of Cambridge, UK)
Helen Jenkins (Un of Wales, Aberystwyth, UK)
Irena Spasic (Center for Integrative Systems Biology, Manchester, UK)
Larissa Soldatova (University of Wales, Aberystwyth, UK)
Philippe Rocca-Serra (EBI and MGED Society)
Susanna-Assunta Sansone (EBI)
People involved in the term creation from ID<1400000:
Joseph Cruz
Daniel Schober
Michael Wilson
Reza Salek
Daniel Jacob
David Wishart
Terms with IDs ID<1400000 that were NOT asserted in the original Wishart obo file were created by Daniel Schober (COSMOS WP2). Its IDs were autogenerated with the Protege ID generator.
Other people that substantially helped in revising the latest and Cosmos governed CV additions were:
Michael Wilson, Wishart Group, Edmonton, Alberta, Canada
Daniel Jacob, INRA, Bordeaux, France
Annick Moing, INRA, Bordeaux, France
Catherine Deborde, INRA, Bordeaux, France
Reza Salek, EBI, Hinxton, UK
Philippe Rocca-Serra, University of Oxford, Oxford, UK
Andrea Porzel, IPB-Halle, Germany
and the COSMOS WP2 team
A paper describing the overall nmrML data standard and CV has been accepted by Analytical Chemistry (Manuscript ID: ac-2017-02795f.R1), title
`nmrML: a community supported open data standard for the description, storage, and exchange of NMR data`, author(s): Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph; Marcu, Ana; Grant, Jason; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy; Hao, Jie; Ludwig, Christian; Günther, Ulrich; Rosato, Antonio; Klein, Matthias; Lewis, Ian; Luchinat, Claudio; Jones, Andrew; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark; Wishart, David; Steinbeck, Christoph; Salek, Reza; Neumann, Steffen</dc:contributor>
<dc:contributor xml:lang="en">Steffen Neumann</dc:contributor>
<dc:contributor xml:lang="en">Susanna-Assunta Sansone</dc:contributor>
<dc:contributor>Alan Ruttenberg</dc:contributor>
<dc:contributor>Albert Goldfain</dc:contributor>
<dc:contributor>Barry Smith</dc:contributor>
<dc:contributor>Bill Duncan</dc:contributor>
<dc:contributor>Bjoern Peters</dc:contributor>
<dc:contributor>Chris Mungall</dc:contributor>
<dc:contributor>David Osumi-Sutherland</dc:contributor>
<dc:contributor>Fabian Neuhaus</dc:contributor>
<dc:contributor>Holger Stenzhorn</dc:contributor>
<dc:contributor>James A. Overton</dc:contributor>
<dc:contributor>Janna Hastings</dc:contributor>
<dc:contributor>Jie Zheng</dc:contributor>
<dc:contributor>Jonathan Bona</dc:contributor>
<dc:contributor>Larry Hunter</dc:contributor>
<dc:contributor>Leonard Jacuzzo</dc:contributor>
<dc:contributor>Ludger Jansen</dc:contributor>
<dc:contributor>Mark Ressler</dc:contributor>
<dc:contributor>Mathias Brochhausen</dc:contributor>
<dc:contributor>Mauricio Almeida</dc:contributor>
<dc:contributor>Melanie Courtot</dc:contributor>
<dc:contributor>Pierre Grenon</dc:contributor>
<dc:contributor>Randall Dipert</dc:contributor>
<dc:contributor>Ron Rudnicki</dc:contributor>
<dc:contributor>Selja Seppälä</dc:contributor>
<dc:contributor>Stefan Schulz</dc:contributor>
<dc:contributor>Teresa Fan</dc:contributor>
<dc:contributor>Thomas Bittner</dc:contributor>
<dc:contributor>Vitaly Selivanov</dc:contributor>
<dc:contributor>Werner Ceusters</dc:contributor>
<dc:contributor>Yongqun "Oliver" He</dc:contributor>
<dc:coverage xml:lang="en">Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open access nmrML XML format developed by the COSMOS EU project.</dc:coverage>
<dc:creator>Philippe Rocca-Serra</dc:creator>
<dc:description xml:lang="en">an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.</dc:description>
<dc:format xml:lang="en">OWL</dc:format>
<dc:format>OWL</dc:format>
<dc:license xml:lang="en">https://creativecommons.org/licenses/by/4.0/</dc:license>
<dc:rights>http://creativecommons.org/licenses/by/3.0/</dc:rights>
<dc:title xml:lang="en">Metabolomics Standards Initiative Ontology (MSIO)</dc:title>
<dc:title xml:lang="en">nuclear magnetic resonance CV</dc:title>
<terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
<pav:importedFrom>https://raw.githubusercontent.com/jmillanacosta/MSIO/master/MSIO-edit.owl</pav:importedFrom>
<doap:audience xml:lang="en">This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments.</doap:audience>
<doap:bug-database xml:lang="en">https://github.com/nmrML/nmrML/issues</doap:bug-database>
<doap:documenter xml:lang="en">Daniel Schober</doap:documenter>
<doap:implements xml:lang="en">https://github.com/nmrML/nmrML</doap:implements>
<doap:location xml:lang="en">https://github.com/nmrML/nmrML/tree/master/ontologies</doap:location>
<doap:mailing-list xml:lang="en">https://groups.google.com/forum/?hl=en#!forum/nmrml/join</doap:mailing-list>
<doap:maintainer xml:lang="en">http://www.metabolomics-msi.org/
http://phenomenal-h2020.eu/home/
http://www.cosmos-fp7.eu/WP2</doap:maintainer>
<oboInOwl:auto-generated-by xml:lang="en">OBO-Edit 2.2</oboInOwl:auto-generated-by>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:created_by xml:lang="en">Daniel Schober</oboInOwl:created_by>
<oboInOwl:creation_date xml:lang="en">2017-10-19T10:11:26Z</oboInOwl:creation_date>
<oboInOwl:date>2025-03-01 02:03:55</oboInOwl:date>
<rdfs:comment xml:lang="en">Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.</rdfs:comment>
<rdfs:comment xml:lang="en">The BSD license on the BFO project site refers to code used to build BFO.</rdfs:comment>
<rdfs:comment xml:lang="en">This version (1.1.0) uses the Basic Formal Ontology (BFO) as its top level ontology. We might at some point close the resulting semantic gap by using OBI and IAO as intermediate bridges.</rdfs:comment>
<rdfs:comment>This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo/dev/bfo.clif"/>
<rdfs:isDefinedBy rdf:resource="https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/"/>
<rdfs:seeAlso rdf:resource="http://groups.google.com/group/bfo-devel"/>
<rdfs:seeAlso rdf:resource="http://groups.google.com/group/bfo-discuss"/>
<rdfs:seeAlso rdf:resource="http://groups.google.com/group/bfo-owl-devel"/>
<rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/bfo/dev/owl"/>
<rdfs:seeAlso rdf:resource="https://github.com/BFO-ontology/BFO/tree/master/src/tools/"/>
<owl:deprecated xml:lang="en">http://www.metabolomicscentre.ca/nmrML/msi-nmr.obo</owl:deprecated>
<owl:versionInfo xml:lang="en">1.1.0</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">1.0</owl:versionInfo>
<owl:versionInfo>This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.</owl:versionInfo>
<foaf:homepage rdf:resource="http://basic-formal-ontology.org/"/>
<foaf:homepage rdf:resource="http://ifomis.org/bfo"/>
<foaf:homepage rdf:resource="https://github.com/BFO-ontology/BFO"/>
<foaf:homepage xml:lang="en">http://nmrml.org/cv/</foaf:homepage>
<foaf:mbox rdf:resource="mailto:[email protected]"/>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://protege.stanford.edu/plugins/owl/protege#defaultLanguage -->
<owl:AnnotationProperty rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000179 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000179">
<obo:IAO_0000115 xml:lang="en">Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.</obo:IAO_0000115>
<obo:IAO_0000232 xml:lang="en">Really of interest to developers only</obo:IAO_0000232>
<rdfs:label xml:lang="en">BFO OWL specification label</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000180 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000180">
<obo:IAO_0000115 xml:lang="en">Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2</obo:IAO_0000115>
<obo:IAO_0000119>Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">Really of interest to developers only</obo:IAO_0000232>
<rdfs:label xml:lang="en">BFO CLIF specification label</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor preferred term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">term editor</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">alternative term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">definition source</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">imported from</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000600 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">elucidation</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000601 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000601">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">has associated axiom(nl)</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000602 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000602">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">has associated axiom(fol)</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0010000 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0010000">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">has axiom label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
<!-- http://purl.org/dc/elements/1.1/coverage -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/coverage"/>
<!-- http://purl.org/dc/elements/1.1/creator -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>
<!-- http://purl.org/dc/elements/1.1/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
<!-- http://purl.org/dc/elements/1.1/format -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/format"/>
<!-- http://purl.org/dc/elements/1.1/identifier -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/identifier"/>
<!-- http://purl.org/dc/elements/1.1/language -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/language"/>
<!-- http://purl.org/dc/elements/1.1/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/license"/>
<!-- http://purl.org/dc/elements/1.1/member -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/member"/>
<!-- http://purl.org/dc/elements/1.1/publisher -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/publisher"/>
<!-- http://purl.org/dc/elements/1.1/relation -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/relation"/>
<!-- http://purl.org/dc/elements/1.1/rights -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/rights"/>
<!-- http://purl.org/dc/elements/1.1/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
<!-- http://purl.org/dc/elements/1.1/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
<!-- http://purl.org/dc/elements/1.1/type -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://purl.org/pav/importedFrom -->
<owl:AnnotationProperty rdf:about="http://purl.org/pav/importedFrom"/>
<!-- http://usefulinc.com/ns/doap#audience -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#audience"/>
<!-- http://usefulinc.com/ns/doap#bug-database -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#bug-database"/>
<!-- http://usefulinc.com/ns/doap#documenter -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#documenter"/>
<!-- http://usefulinc.com/ns/doap#implements -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#implements"/>
<!-- http://usefulinc.com/ns/doap#location -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#location"/>
<!-- http://usefulinc.com/ns/doap#mailing-list -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#mailing-list"/>
<!-- http://usefulinc.com/ns/doap#maintainer -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#maintainer"/>
<!-- http://usefulinc.com/ns/doap#revision -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#revision"/>
<!-- http://www.geneontology.org/formats/oboInOwl#auto-generated-by -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#auto-generated-by"/>
<!-- http://www.geneontology.org/formats/oboInOwl#consider -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#consider"/>
<!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
<!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date"/>
<!-- http://www.geneontology.org/formats/oboInOwl#date -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#date"/>
<!-- http://www.geneontology.org/formats/oboInOwl#default-namespace -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#default-namespace"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label xml:lang="en">database_cross_reference</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
<rdfs:label xml:lang="en">has_exact_synonym</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion">
<rdfs:label xml:lang="en">has_obo_format_version</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace">
<rdfs:label xml:lang="en">has_obo_namespace</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#id -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
<!-- http://www.geneontology.org/formats/oboInOwl#saved-by -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#saved-by"/>
<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"/>
<!-- http://www.w3.org/2000/01/rdf-schema#comment -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
<!-- http://www.w3.org/2000/01/rdf-schema#isDefinedBy -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#isDefinedBy"/>
<!-- http://www.w3.org/2000/01/rdf-schema#label -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<!-- http://www.w3.org/2000/01/rdf-schema#seeAlso -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#seeAlso"/>
<!-- http://www.w3.org/2004/02/skos/core#altLabel -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>
<!-- http://www.w3.org/2004/02/skos/core#definition -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<!-- http://www.w3.org/2004/02/skos/core#editorialNote -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#editorialNote"/>
<!-- http://www.w3.org/2004/02/skos/core#example -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#example"/>
<!-- http://www.w3.org/2004/02/skos/core#note -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#note"/>
<!-- http://www.w3.org/2004/02/skos/core#scopeNote -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#scopeNote"/>
<!-- http://xmlns.com/foaf/0.1/homepage -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
<!-- http://xmlns.com/foaf/0.1/mbox -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/mbox"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/MSIO_0000175 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MSIO_0000175">
<rdfs:subClassOf rdf:resource="http://www.bioassayontology.org/bao#BAO_0002116"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a "lethal dose" represents a dose (usually recorded as dose per kilogram of subject body weight) at which a given percentage of subjects will die.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">EU H2020 PhenoMenAl</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Lethal_dose</obo:IAO_0000119>
<rdfs:label xml:lang="en">lethal dose</rdfs:label>
</owl:Class>
<!-- http://www.bioassayontology.org/bao#BAO_0002116 -->
<owl:Class rdf:about="http://www.bioassayontology.org/bao#BAO_0002116"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Individuals
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000002 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000002">
<rdfs:label xml:lang="en">example to be eventually removed</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000103 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000103">
<obo:IAO_0000115 xml:lang="en">The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job</obo:IAO_0000115>
<obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">failed exploratory term</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000120 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000120">
<obo:IAO_0000115 xml:lang="en">Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.</obo:IAO_0000115>
<rdfs:label xml:lang="en">metadata complete</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000121 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000121">
<obo:IAO_0000115 xml:lang="en">term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
<rdfs:label xml:lang="en">organizational term</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000122 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000122">
<obo:IAO_0000115 xml:lang="en">Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."</obo:IAO_0000115>
<rdfs:label xml:lang="en">ready for release</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000123 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000123">
<obo:IAO_0000115 xml:lang="en">Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.</obo:IAO_0000115>
<rdfs:label xml:lang="en">metadata incomplete</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000124 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000124">
<obo:IAO_0000115 xml:lang="en">Nothing done yet beyond assigning a unique class ID and proposing a preferred term.</obo:IAO_0000115>
<rdfs:label xml:lang="en">uncurated</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000125 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000125">
<obo:IAO_0000115 xml:lang="en">All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.</obo:IAO_0000115>
<rdfs:label xml:lang="en">pending final vetting</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000224 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000224">
<obo:IAO_0000115 xml:lang="en">Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
<rdfs:label xml:lang="en">core</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000226 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000226">
<rdfs:label xml:lang="en">placeholder removed</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000227 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000227">
<obo:IAO_0000116 xml:lang="en">An editor note should explain what were the merged terms and the reason for the merge.</obo:IAO_0000116>
<rdfs:label xml:lang="en">terms merged</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000228 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000228">
<obo:IAO_0000116 xml:lang="en">This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.</obo:IAO_0000116>
<rdfs:label xml:lang="en">term imported</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000229 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000229">
<obo:IAO_0000116 xml:lang="en">This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.</obo:IAO_0000116>
<rdfs:label xml:lang="en">term split</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000230 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000230">
<obo:IAO_0000116 xml:lang="en">This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">We expect to be able to mine these new reasons and add instances as required.</obo:IAO_0000116>
<rdfs:label xml:lang="en">other</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000410 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000410">
<obo:IAO_0000116>Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.</obo:IAO_0000116>
<obo:IAO_0000117>Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119>A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf</obo:IAO_0000119>
<rdfs:label>universal</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000420 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000420">
<obo:IAO_0000115>A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal</obo:IAO_0000115>
<obo:IAO_0000116>"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.</obo:IAO_0000116>
<obo:IAO_0000117>Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label>defined class</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000421 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000421">
<obo:IAO_0000115>A named class expression is a logical expression that is given a name. The name can be used in place of the expression.</obo:IAO_0000115>
<obo:IAO_0000116>named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions</obo:IAO_0000116>
<obo:IAO_0000117>Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label>named class expression</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000423 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000423">
<obo:IAO_0000115 xml:lang="en">Terms with this status should eventually replaced with a term from another ontology.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<rdfs:label xml:lang="en">to be replaced with external ontology term</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000428 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000428">
<obo:IAO_0000115 xml:lang="en">A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<rdfs:label xml:lang="en">requires discussion</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/MSIO_0000068 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/MSIO_0000068">
<obo:IAO_0000115 xml:lang="en">Biocrates Life Sciences AG, a biotechnology company, develops and markets targeted metabolic phenotyping solutions that support the discovery and validation of biomarkers for complex multifactorial diseases in pre-clinical and clinical research. The company offers mass-spectrometry based reproducible and quantitative kits and services that analyze various endogenous metabolites; and tools for insight into pathways and metabolic signatures of diseases, such as cancer or neurodegenerative diseases. It also offers metabolic phenotyping, and biomarker discovery and development services.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Biocrates Life Sciences AG</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">https://www.bloomberg.com/research/stocks/private/snapshot.asp?privcapId=20741978</obo:IAO_0000119>