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NIAID-GSC-BRC.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi/NIAID-GSC-BRC.owl#"
xml:base="http://purl.obolibrary.org/obo/obi/NIAID-GSC-BRC.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: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:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi/NIAID-GSC-BRC.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/obi/2025-01-09/NIAID-GSC-BRC.owl"/>
<protege:defaultLanguage>en</protege:defaultLanguage>
<dc:contributor xml:lang="en">Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester</dc:contributor>
<dc:creator xml:lang="en">Alan Ruttenberg</dc:creator>
<dc:creator xml:lang="en">Allyson Lister</dc:creator>
<dc:creator xml:lang="en">Barry Smith</dc:creator>
<dc:creator xml:lang="en">Bill Bug</dc:creator>
<dc:creator xml:lang="en">Bjoern Peters</dc:creator>
<dc:creator xml:lang="en">Carlo Torniai</dc:creator>
<dc:creator xml:lang="en">Chris Mungall</dc:creator>
<dc:creator xml:lang="en">Chris Stoeckert</dc:creator>
<dc:creator xml:lang="en">Chris Taylor</dc:creator>
<dc:creator xml:lang="en">Christian Bolling</dc:creator>
<dc:creator xml:lang="en">Cristian Cocos</dc:creator>
<dc:creator xml:lang="en">Daniel Rubin</dc:creator>
<dc:creator xml:lang="en">Daniel Schober</dc:creator>
<dc:creator xml:lang="en">Dawn Field</dc:creator>
<dc:creator xml:lang="en">Dirk Derom</dc:creator>
<dc:creator xml:lang="en">Elisabetta Manduchi</dc:creator>
<dc:creator xml:lang="en">Eric Deutsch</dc:creator>
<dc:creator xml:lang="en">Frank Gibson</dc:creator>
<dc:creator xml:lang="en">Gilberto Fragoso</dc:creator>
<dc:creator xml:lang="en">Helen C. Causton</dc:creator>
<dc:creator xml:lang="en">Helen Parkinson</dc:creator>
<dc:creator xml:lang="en">Holger Stenzhorn</dc:creator>
<dc:creator xml:lang="en">James A. Overton</dc:creator>
<dc:creator xml:lang="en">James Malone</dc:creator>
<dc:creator xml:lang="en">Jay Greenbaum</dc:creator>
<dc:creator xml:lang="en">Jeffrey Grethe</dc:creator>
<dc:creator xml:lang="en">Jennifer Fostel</dc:creator>
<dc:creator xml:lang="en">Jessica Turner</dc:creator>
<dc:creator xml:lang="en">Jie Zheng</dc:creator>
<dc:creator xml:lang="en">Joe White</dc:creator>
<dc:creator xml:lang="en">John Westbrook</dc:creator>
<dc:creator xml:lang="en">Kevin Clancy</dc:creator>
<dc:creator xml:lang="en">Larisa Soldatova</dc:creator>
<dc:creator xml:lang="en">Lawrence Hunter</dc:creator>
<dc:creator xml:lang="en">Liju Fan</dc:creator>
<dc:creator xml:lang="en">Luisa Montecchi</dc:creator>
<dc:creator xml:lang="en">Matthew Brush</dc:creator>
<dc:creator xml:lang="en">Matthew Pocock</dc:creator>
<dc:creator xml:lang="en">Melanie Courtot</dc:creator>
<dc:creator xml:lang="en">Melissa Haendel</dc:creator>
<dc:creator xml:lang="en">Mervi Heiskanen</dc:creator>
<dc:creator xml:lang="en">Monnie McGee</dc:creator>
<dc:creator xml:lang="en">Norman Morrison</dc:creator>
<dc:creator xml:lang="en">Philippe Rocca-Serra</dc:creator>
<dc:creator xml:lang="en">Phillip Lord</dc:creator>
<dc:creator xml:lang="en">Pierre Grenon</dc:creator>
<dc:creator xml:lang="en">Richard Bruskiewich</dc:creator>
<dc:creator xml:lang="en">Richard Scheuermann</dc:creator>
<dc:creator xml:lang="en">Robert Stevens</dc:creator>
<dc:creator xml:lang="en">Ryan R. Brinkman</dc:creator>
<dc:creator xml:lang="en">Stefan Wiemann</dc:creator>
<dc:creator xml:lang="en">Susanna-Assunta Sansone</dc:creator>
<dc:creator xml:lang="en">Tanya Gray</dc:creator>
<dc:creator xml:lang="en">Tina Hernandez-Boussard</dc:creator>
<dc:creator xml:lang="en">Trish Whetzel</dc:creator>
<dc:creator xml:lang="en">Yongqun He</dc:creator>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2009-07-31</dc:date>
<dc:description xml:lang="en">A subset of OBI containing all terms specified by the NIAID GSCID and BRC Project, Sample and Sequencing Assay Core Metadata Standards. This OBI view includes NIAID GSCID and BRC community preferred labels and field IDs specified in the standards (https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards).</dc:description>
<dc:format xml:lang="en">OWL-DL</dc:format>
<dc:subject xml:lang="en">An ontology for the annotation of biomedical and functional genomics experiments.</dc:subject>
<terms:license>http://creativecommons.org/licenses/by/4.0/</terms:license>
<terms:title>Ontology for Biomedical Investigations</terms:title>
<rdfs:comment>Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.</rdfs:comment>
<owl:versionInfo>2025-01-09</owl:versionInfo>
</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>
</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>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
<obo:IAO_0000111 xml:lang="en">editor preferred label</obo:IAO_0000111>
<obo:IAO_0000111>editor preferred term</obo:IAO_0000111>
<obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
<obo:IAO_0000111>editor preferred term~editor preferred label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor preferred label</rdfs:label>
<rdfs:label>editor preferred term</rdfs:label>
<rdfs:label xml:lang="en">editor preferred term</rdfs:label>
<rdfs:label>editor preferred term~editor preferred label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
<obo:IAO_0000111 xml:lang="en">example of usage</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">example of usage</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
<obo:IAO_0000111 xml:lang="en">has curation status</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<rdfs:label xml:lang="en">has curation status</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<obo:IAO_0000111>definition</obo:IAO_0000111>
<obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
<obo:IAO_0000111>textual definition</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label>definition</rdfs:label>
<rdfs:label xml:lang="en">definition</rdfs:label>
<rdfs:label>textual definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
<obo:IAO_0000111 xml:lang="en">editor note</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obofoundry.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
<obo:IAO_0000111 xml:lang="en">term editor</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<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">
<obo:IAO_0000111 xml:lang="en">alternative label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.</obo:IAO_0000115>
<obo:IAO_0000117>OBO Operations committee</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:comment>Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">alternative label</rdfs:label>
<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">
<obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></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">
<obo:IAO_0000111 xml:lang="en">curator note</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An administrative note of use for a curator but of no use for a user</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">curator note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
<obo:IAO_0000111 xml:lang="en">imported from</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">For external terms/classes, the ontology from which the term was imported</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>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<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_0000589 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000589"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000600 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
<obo:IAO_0000111 xml:lang="en">elucidation</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Barry Smith</obo:IAO_0000119>
<obo:IAO_0000600 xml:lang="en">Primitive terms in a highest-level ontology such as BFO are terms which 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_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">
<obo:IAO_0000111 xml:lang="en">has associated axiom(nl)</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000600 xml:lang="en">An axiom associated with a term expressed using natural language</obo:IAO_0000600>
<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">
<obo:IAO_0000111 xml:lang="en">has associated axiom(fol)</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000600 xml:lang="en">An axiom expressed in first order logic using CLIF syntax</obo:IAO_0000600>
<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/OBI_GSCID_BRC_Field_ID -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OBI_GSCID_BRC_Field_ID"/>
<!-- http://purl.obolibrary.org/obo/RO_0001900 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900"/>
<!-- 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/creator -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>
<!-- http://purl.org/dc/elements/1.1/date -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>
<!-- 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/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
<!-- http://purl.org/dc/elements/1.1/subject -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/subject"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://purl.org/dc/terms/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/source"/>
<!-- http://purl.org/dc/terms/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Datatypes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.w3.org/2000/01/rdf-schema#Literal -->
<rdfs:Datatype rdf:about="http://www.w3.org/2000/01/rdf-schema#Literal"/>
<!-- http://www.w3.org/2001/XMLSchema#date -->
<rdfs:Datatype rdf:about="http://www.w3.org/2001/XMLSchema#date"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">is part of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my brain is part of my body (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this day is part of this year (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a part and its whole</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
<rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">has part</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my body has part my brain (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this year has part this day (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a whole and its part</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000054 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000054">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000111 xml:lang="en">realized in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this disease is realized in this disease course</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this fragility is realized in this shattering</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigator role is realized in this investigation</obo:IAO_0000112>
<obo:IAO_0000118 xml:lang="en">is realized by</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">realized_in</obo:IAO_0000118>
<obo:IAO_0000600 xml:lang="en">[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
<rdfs:comment>Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">realized in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000055 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:IAO_0000111 xml:lang="en">realizes</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this disease course realizes this disease</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigation realizes this investigator role</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this shattering realizes this fragility</obo:IAO_0000112>
<obo:IAO_0000600 xml:lang="en">to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
<rdfs:comment>Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">realizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000039 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000039">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<obo:IAO_0000111 xml:lang="en">has measurement unit label</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">has measurement unit label</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<obo:IAO_0000111 xml:lang="en">is about</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A (currently) primitive relation that relates an information artifact to an entity.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">is about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000219 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000219">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<obo:IAO_0000111 xml:lang="en">denotes</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">denotes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000221 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000221">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<obo:IAO_0000111 xml:lang="en">is quality measurement of</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">is quality measurement of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000107 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000107">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0001173"/>
<obo:IAO_0000111>provides_service_consumer_with</obo:IAO_0000111>
<obo:IAO_0000112>The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.</obo:IAO_0000115>
<rdfs:label>provides_service_consumer_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000124 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000124">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0001909"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111>is_supported_by_data</obo:IAO_0000111>
<obo:IAO_0000112>The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process</obo:IAO_0000115>
<obo:IAO_0000117>OBI</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<obo:IAO_0000119>Philly 2011 workshop</obo:IAO_0000119>
<rdfs:label>is_supported_by_data</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000293 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>has specified input</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">see is_input_of example_of_usage</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The inverse property of is specified input of</obo:IAO_0000115>
<obo:IAO_0000116>8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Melanie Coutot</obo:IAO_0000117>
<rdfs:label xml:lang="en">has specified input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000295 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000295">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>is specified input of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<rdfs:label xml:lang="en">is specified input of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>has specified output</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The inverse property of is specified output of</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Melanie Courtot</obo:IAO_0000117>
<rdfs:label xml:lang="en">has specified output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000312 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>is specified output of</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<rdfs:label xml:lang="en">is specified output of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000417 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000417">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000833"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111>achieves_planned_objective</obo:IAO_0000111>
<obo:IAO_0000112>A cell sorting process achieves the objective specification 'material separation objective'</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.</obo:IAO_0000115>
<obo:IAO_0000117>BP, AR, PPPB branch</obo:IAO_0000117>
<obo:IAO_0000119>PPPB branch derived</obo:IAO_0000119>
<obo:IAO_0000232>modified according to email thread from 1/23/09 in accordince with DT and PPPB branch</obo:IAO_0000232>
<rdfs:label>achieves_planned_objective</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000643 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000643">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<obo:IAO_0000111>has grain</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119>PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349</obo:IAO_0000119>
<rdfs:label>has grain</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000646 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000646">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000647"/>
<obo:IAO_0000111>provisions</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use</obo:IAO_0000115>
<obo:IAO_0000116>5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship.</obo:IAO_0000116>
<obo:IAO_0000117>GROUP: Relations branch</obo:IAO_0000117>
<obo:IAO_0000118>supplies</obo:IAO_0000118>
<rdfs:label>provisions</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000647 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000647">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000245"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000111>has_supplier</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Alan Rutternberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Cristian Cocos</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Melanie Courtot</obo:IAO_0000117>
<rdfs:label>has_supplier</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000833 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000833">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>objective_achieved_by</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.</obo:IAO_0000115>
<obo:IAO_0000117>OBI</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<rdfs:label>objective_achieved_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000846 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000846">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001688"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000245"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
<obo:IAO_0000111>is member of organization</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.</obo:IAO_0000115>
<obo:IAO_0000116>2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population</obo:IAO_0000116>
<obo:IAO_0000116>JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.</obo:IAO_0000116>
<obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>Person:Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000119>Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000119>Person:Helen Parkinson</obo:IAO_0000119>
<obo:IAO_0000232>2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000232>
<rdfs:label>is member of organization</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001688 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001688">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000245"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000111 xml:lang="en">has organization member</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Relating an organization to a legal person or organization.</obo:IAO_0000115>
<obo:IAO_0000116>See tracker:
https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178</obo:IAO_0000116>
<obo:IAO_0000117>Person: Jie Zheng</obo:IAO_0000117>
<rdfs:label xml:lang="en">has organization member</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001938 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001938">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<obo:IAO_0000111>has value specification</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A relation between an information content entity and a value specification that specifies its value.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: James A. Overton</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<rdfs:label>has value specification</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000052 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000052">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<obo:IAO_0000111 xml:lang="en">inheres in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this fragility is a characteristic of this vase</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this red color is a characteristic of this apple</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">inheres_in</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:comment>Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.</rdfs:comment>
<rdfs:label xml:lang="en">characteristic of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000053 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000111 xml:lang="en">bearer of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this apple is bearer of this red color</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this vase is bearer of this fragility</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">Inverse of characteristic_of</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">bearer_of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">is bearer of</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">has characteristic</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">participates in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood clot participates in this blood coagulation</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this input material (or this output material) participates in this process</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigator participates in this investigation</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">participates_in</obo:IAO_0000118>
<rdfs:label xml:lang="en">participates in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000111 xml:lang="en">has participant</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood coagulation has participant this blood clot</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigation has participant this investigator</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this process has participant this input material (or this output material)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a process and a continuant, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_participant</obo:IAO_0000118>
<terms:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</terms:source>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000058 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is concretized as</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000059 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
<rdfs:label xml:lang="en">concretizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000079 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000079">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000112 xml:lang="en">this catalysis function is a function of this enzyme</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">function_of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">is function of</obo:IAO_0000118>
<rdfs:comment>This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.</rdfs:comment>
<rdfs:label xml:lang="en">function of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000080 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000080">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
<obo:IAO_0000112 xml:lang="en">this red color is a quality of this apple</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A quality inheres in its bearer at all times for which the quality exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is quality of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">quality_of</obo:IAO_0000118>
<rdfs:comment>This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.</rdfs:comment>
<rdfs:label xml:lang="en">quality of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000081 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000081">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<obo:IAO_0000112 xml:lang="en">this investigator role is a role of this person</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is role of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">role_of</obo:IAO_0000118>
<rdfs:comment>This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.</rdfs:comment>
<rdfs:label xml:lang="en">role of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000085 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000085">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000112 xml:lang="en">this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_function</obo:IAO_0000118>
<rdfs:label xml:lang="en">has function</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000086 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000086">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000112 xml:lang="en">this apple has quality this red color</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence</obo:IAO_0000115>