wc_onto/ontologies/SEPIO.owl
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/sepio.owl#"
xml:base="http://purl.obolibrary.org/obo/sepio.owl"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/sepio.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/sepio-v20170929.owl"/>
<rdfs:seeAlso>The SEPIO ontology is in its early stages of development, undergoing iterative refine,ent as new requirements emerge and alignment wiht existing standards is explored. The SEPIO core file imports two files which can be resolved at the URLs below:
IAO ontology-metadata import: https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/imports/ontology-metadata.owl
bfo mireot: https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/mireots/bfo.owl</rdfs:seeAlso>
<obo:IAO_0000116>BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. 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 [17</obo:IAO_0000116>
<dc:contributor>Ron Rudnicki</dc:contributor>
<dc:contributor>Barry Smith</dc:contributor>
<dc:contributor>Larry Hunter</dc:contributor>
<dc:contributor>Werner Ceusters</dc:contributor>
<dc:contributor>Jonathan Bona</dc:contributor>
<dc:contributor>Robert Rovetto</dc:contributor>
<dc:contributor>Albert Goldfain</dc:contributor>
<dc:contributor>Melanie Courtot</dc:contributor>
<dc:contributor>Alan Ruttenberg</dc:contributor>
<rdfs:seeAlso rdf:resource="http://groups.google.com/group/bfo-owl-devel"/>
<dc:contributor>Chris Mungall</dc:contributor>
<dc:license rdf:resource="http://creativecommons.org/licenses/by/3.0/"/>
<rdfs:seeAlso rdf:resource="http://bfo.googlecode.com/svn/trunk/src/tools/"/>
<dc:contributor>Matthew Brush</dc:contributor>
<dc:contributor>David Osumi-Sutherland</dc:contributor>
<rdfs:isDefinedBy rdf:resource="http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/"/>
<dc:contributor>James A. Overton</dc:contributor>
<foaf:mbox rdf:resource="mailto:bfo-owl-devel@googlegroups.com"/>
<dc:contributor>Fabian Neuhaus</dc:contributor>
<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 [30</obo:IAO_0000116>
<foaf:homepage rdf:resource="http://code.google.com/p/bfo/"/>
<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 one such 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>
<owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
<rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/bfo/dev/owl"/>
<dc:contributor>Mathias Brochhausen</dc:contributor>
<dc:contributor>Janna Hastings</dc:contributor>
<dc:contributor>Leonard Jacuzzo</dc:contributor>
<dc:contributor>Randall Dipert</dc:contributor>
<dc:contributor>Stefan Schulz</dc:contributor>
<foaf:homepage rdf:resource="http://ifomis.org/bfo"/>
<rdfs:seeAlso rdf:resource="http://groups.google.com/group/bfo-devel"/>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo/2014-05-03/ReleaseNotes"/>
<dc:contributor>Yongqun "Oliver" He</dc:contributor>
<dc:contributor>Bjoern Peters</dc:contributor>
<dc:contributor>Bill Duncan</dc:contributor>
<dc:contributor>Ludger Jansen</dc:contributor>
<dc:contributor>Thomas Bittner</dc:contributor>
<rdfs:seeAlso rdf:resource="http://groups.google.com/group/bfo-discuss"/>
<dc:contributor>Jie Zheng</dc:contributor>
<dc:contributor>Mauricio Almeida</dc:contributor>
<dc:contributor>Mark Ressler</dc:contributor>
<rdfs:comment xml:lang="en">This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/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 http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/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 http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl.
If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies.
See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1.</rdfs:comment>
<dc:contributor>Pierre Grenon</dc:contributor>
<protege:defaultLanguage rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo/dev/bfo.clif"/>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo/2012-07-20/Reference"/>
</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">
<obo:IAO_0000111 xml:lang="en">editor preferred term</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 term</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</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 class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not</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_0000113 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
<obo:IAO_0000111 xml:lang="en">in branch</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">GROUP:OBI</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000277</obo:IAO_0000119>
<rdfs:label xml:lang="en">in branch</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>
<obo:IAO_0000119 xml:lang="en">OBI_0000281</obo:IAO_0000119>
<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 xml:lang="en">definition</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<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 xml:lang="en">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.obfoundry.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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=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 term</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)</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">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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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_0000231 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231">
<obo:IAO_0000111 xml:lang="en">has obsolescence reason</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.</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">has obsolescence reason</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_0000411 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000411">
<obo:IAO_0000111 xml:lang="en">is denotator type</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">relates an class defined in an ontology, to the type of it's denotator</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is denotator type</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_0000424 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000424">
<obo:IAO_0000111 xml:lang="en">expand expression to</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chris Mungall</obo:IAO_0000117>
<rdfs:label xml:lang="en">expand expression to</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000425 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000425">
<obo:IAO_0000111 xml:lang="en">expand assertion to</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
<rdfs:label xml:lang="en">expand assertion to</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000426 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000426">
<obo:IAO_0000111 xml:lang="en">first order logic expression</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">first order logic expression</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000427 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000427">
<obo:IAO_0000111 xml:lang="en">antisymmetric property</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">part_of antisymmetric property xsd:true</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">use boolean value xsd:true to indicate that the property is an antisymmetric property</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">antisymmetric property</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000589 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000589">
<obo:IAO_0000111 xml:lang="en">OBO foundry unique label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An alternative name for a class or property which is unique across the OBO Foundry.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBO Foundry <http://obofoundry.org/></obo:IAO_0000119>
<rdfs:label xml:lang="en">OBO foundry unique label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000596 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000596">
<obo:IAO_0000112>Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"</obo:IAO_0000112>
<obo:IAO_0000115>Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)</obo:IAO_0000115>
<obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">has ID digit count</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000597 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000597">
<obo:IAO_0000112>Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
</obo:IAO_0000112>
<obo:IAO_0000115>Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms</obo:IAO_0000115>
<obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">has ID range allocated to</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000598 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000598">
<obo:IAO_0000112>Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"</obo:IAO_0000112>
<obo:IAO_0000115>Relating an ontology used to record id policy to the ontology namespace whose policy it manages</obo:IAO_0000115>
<obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label>has ID policy for</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000599 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000599">
<obo:IAO_0000112>Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"</obo:IAO_0000112>
<obo:IAO_0000115>Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.</obo:IAO_0000115>
<obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">has ID prefix</rdfs:label>
</owl:AnnotationProperty>
<!-- 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/IAO_0000603 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000603">
<obo:IAO_0000111 xml:lang="en">is allocated id range</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">Add as annotation triples in the granting ontology</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">is allocated id range</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0010000 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0010000">
<obo:IAO_0000111 xml:lang="en">has axiom id</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">A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI</obo:IAO_0000600>
<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.obolibrary.org/obo/IAO_0100001 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001">
<obo:IAO_0000111 xml:lang="en">term replaced by</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Add as annotation triples in the granting ontology</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">Use on obsolete terms, relating the term to another term that can be used as a substitute</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
<rdfs:label xml:lang="en">term replaced by</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000052 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000052">
<rdfs:label xml:lang="en">consider</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000061 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000061">
<rdfs:label xml:lang="en">SEPIO_editor_note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000184 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000184">
<rdfs:label xml:lang="en">usage note</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/member -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/member"/>
<!-- http://purl.org/dc/terms/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description">
<obo:IAO_0000115>An account of the resource.</obo:IAO_0000115>
<rdfs:comment xml:lang="en">Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."</rdfs:comment>
<rdfs:label xml:lang="en">description</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/terms/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/source">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:AnnotationProperty>
<!-- 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#inSubset -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"/>
<!-- 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#seeAlso -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#seeAlso"/>
<!-- http://xmlns.com/foaf/0.1/homepage -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// 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 https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
</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 https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000055 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<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:label>realizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>Is_about is a (currently) primitive relation that relates an information artifact to an entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000999 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000999">
<obo:IAO_0000115>A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.</obo:IAO_0000115>
<rdfs:label>has_category_label</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>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<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>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002233 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002233">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002352"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>consumes</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">has input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002234 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002234">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002353"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>produces</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">has output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002350 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002350">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<obo:IAO_0000115>Is member of is a mereological relation between a item and a collection.</obo:IAO_0000115>
<rdfs:label>member of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002352 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002352">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">input of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002353 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002353">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">output of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002614 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002614">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<obo:IAO_0000115>A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.</obo:IAO_0000115>
<obo:IAO_0000118>is_evidence_with_support_from</obo:IAO_0000118>
<rdfs:label xml:lang="en">is_evidence_supported_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000006 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<obo:IAO_0000115>A relationship between an assertion or proposition and an evidence line used in evaluating its validity.</obo:IAO_0000115>
<obo:IAO_0000116>Consider re-use of http://purl.obolibrary.org/obo/RO_0002558 ! 'has evidence'.
Definition = "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x."
See also http://semanticscience.org/resource/SIO_000772 ! 'has evidence'.</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000007 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000007">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000098"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000007"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a proposition and information that supports its validity, based on the evaluation of some agent.</obo:IAO_0000115>
<obo:IAO_0000116>Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000206 ! 'is supported by'</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_supporting_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000008 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000008">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000007"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a proposition and information that contradicts its validity, based on the evaluation and conclusion of some agent.</obo:IAO_0000115>
<obo:IAO_0000116>Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000774 ! 'is refuted by'</obo:IAO_0000116>
<obo:IAO_0000118>has_conflicting_evidence</obo:IAO_0000118>
<obo:IAO_0000118>has_refuting_evidence_line</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_disputing_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000009 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000009">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000098"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000009"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a proposition and information that was used to evaluate a particular proposition, but failed to provide conclusive support for or against its validity.</obo:IAO_0000115>
<obo:IAO_0000116>Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000207 ! 'is disputed by'</obo:IAO_0000116>
<rdfs:comment>A relation between a proposition and information that does not conclusively support or contradict its validity, based on evaluation of some agent.</rdfs:comment>
<rdfs:label xml:lang="en">has_inconclusive_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000015 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000015">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<obo:SEPIO_0000052>http://purl.org/see/rdo#is_asserted_in_assertion
or
http://purl.org/see/rdo#is_assertion_expressed_in</obo:SEPIO_0000052>
<rdfs:label>is_asserted_in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000017 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000017">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<rdfs:range rdf:resource="http://www.w3.org/ns/prov#Agent"/>
<obo:IAO_0000116>Consider use of http://purl.obolibrary.org/obo/RO_0002217 ! actively participates in.
Definition = "actively participates in y if and only if x participates in y and x realizes some active role"</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_agent</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000026 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000026">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdf:Description rdf:about="http://purl.org/oban/association_has_subject"/>
</owl:propertyChainAxiom>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_subject :thing1).
The assertion_has_subject property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the subject of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_subject).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_has_subject</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000027 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000027">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000027"/>
</owl:propertyChainAxiom>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_object :thing1).
The assertion_has_object property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the object of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_object).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_has_object</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000028 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000028">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdf:Description rdf:about="http://purl.org/oban/association_has_predicate"/>
</owl:propertyChainAxiom>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_predicate :thing1).
The assertion_has_predicate property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the predicate of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_predicate).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_has_predicate</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000030 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<obo:IAO_0000115>A relation holding between an assertion an assertion and the proposition that it puts forth as true.</obo:IAO_0000115>
<obo:SEPIO_0000052>Mapping to related terms:
Consider: http://purl.org/see/rdo#is_assertion_asserting</obo:SEPIO_0000052>
<rdfs:comment>In practice, SEPIO recommends that data is captured at the assertion level, and post-processed as needed to aggregate assertions making the same claim under a single proposition using this property.</rdfs:comment>
<rdfs:label>asserts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000041 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000041">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000255"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000115>A relation holding between an artifact and a methodological specification (e.g. a protocol, guidelines, rule set) that describes how the artifact was generated by some agent.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_specified_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000046 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000046">
<obo:IAO_0000116>Consider RO:0000087 ! has_role (def = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence). However, this property is defined as a relation between an independent continuant and a role. In BFO, dependent continuants (such as information) cannot bear roles.</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_role</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000084 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002614"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000257"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation holding between an evidence line and an individual information entity that contributes to the argument it represents.</obo:IAO_0000115>
<obo:IAO_0000118>has_supporting_information</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_evidence_item</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000085 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000085">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002614"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002353"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation that links an evidence line to any activities (studies, assays, computational tasks, curation) that generated evidence items contributing to it.</obo:IAO_0000115>
<obo:IAO_0000118>has_supporting_process</obo:IAO_0000118>
<obo:IAO_0000118>is_evidence_supported_by_process</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_supporting_activity</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000086 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000086">
<rdfs:label xml:lang="en">DeprecatedObjectProperty</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000098 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000098">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000116"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000118>has_equivalent_proposition</obo:IAO_0000118>
<rdfs:label xml:lang="en">is_equilavent_to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000099 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000099">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000116"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000118 xml:lang="en">has_consistent_proposition</obo:IAO_0000118>
<rdfs:label>is_consistent_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000100 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000100">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000115"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<obo:IAO_0000116>Previosly implemented property chains:
is_asserted_in o strongly_contradicts o asserts -> strongly_contradicts
asserts o strongly_contradicts o is_asserted_in -> strongly_contradicts
But these broke reasoner - "the given hierarchy is not regular" error message". Apparently breaks rule that "in property chains of 3 or larger, the inner property must not also appear as the composite property". (https://arxiv.org/pdf/1212.2902.pdf)</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_contradicting_proposition</obo:IAO_0000118>
<rdfs:comment>Relation between two propositions that make opposing claims (e.g. proposition1 holds that variant1 is pathogenic for disease1, and proposition2 holds that variant1 is benign for disease1).</rdfs:comment>
<rdfs:label xml:lang="en">strongly_contradicts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000101 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000101">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000115"/>
<obo:IAO_0000118 xml:lang="en">has_inconsistent_proposition</obo:IAO_0000118>
<rdfs:label>contradicts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000108 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000108">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000109"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>Relationship between an assertion or proposition and an information resource in which it is expressed (e.g. a publication, report, or database record).</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_expressed_in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000109 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000109">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000115>Relationship between an information artifact (e.g. a publication, report, database record, or specific text within such artifacts) and an assertion or proposition which its content expresses.</obo:IAO_0000115>
<rdfs:label xml:lang="en">expresses</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000113 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000113">
<obo:IAO_0000116>Grouping class to hold exploratory relationships linking assertions or propositions based on the compatability or degree of agreement in their meaning. Has utility toward inferring links between evidence lines and propositions.</obo:IAO_0000116>
<obo:IAO_0000118>has_concordance</obo:IAO_0000118>
<obo:IAO_0000118>propositional relationships</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_compatability</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000114 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000114">
<obo:IAO_0000115>A relation between a planned process and a parameter that it measures as part of an assay or observation.</obo:IAO_0000115>
<rdfs:label>measures_parameter</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000115 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000115">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000113"/>
<rdfs:label xml:lang="en">conflicts_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000116 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000116">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000113"/>
<rdfs:label xml:lang="en">aligns_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000124 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000124">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002614"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000178"/>
</owl:propertyChainAxiom>
<rdfs:label xml:lang="en">has_supporting_reference</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000126 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000126">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000113"/>
<rdfs:label xml:lang="en">is_inconsistent_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000130 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000130">
<rdfs:subPropertyOf rdf:resource="http://purl.org/pav/createdBy"/>
<obo:IAO_0000115>The agent who made the assertion.</obo:IAO_0000115>
<rdfs:comment>If more than one agent involved, consider them collectively as a group or organization.</rdfs:comment>
<rdfs:label xml:lang="en">asserted_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000132 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000132">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<obo:IAO_0000115>A relation describing the degree of support provided by an evidence line for a target assertion or proposition.</obo:IAO_0000115>
<rdfs:comment>The range for this relation is a term from a value partition that enumerates categorical degrees of strength. Different systems can define terms representing the levels of strength they which to define for their use case.</rdfs:comment>
<rdfs:label xml:lang="en">evidence_has_strength</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000140 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000140">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000150"/>
<obo:IAO_0000118 xml:lang="en">assessed_by</obo:IAO_0000118>
<rdfs:label>evaluated_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000144 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000144">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<obo:IAO_0000115>A relation used to indicate context in which a particular assertion or proposition applies.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_qualifier</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000145 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000145">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.org/dc/terms/source"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000124"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation used to link an assertion or proposition to publications where evidence for it was found.</obo:IAO_0000115>
<rdfs:comment>This is a shortcut relation to be used when publications are referenced as providing support for an assertion, but it is not clear how many evidence lines are described across these publications. In such cases, discrete evidence lines cannot be created, and the has_evidence_from_source relation is used to directly link the assertion to publications providing some form of evidence information.</rdfs:comment>
<rdfs:label xml:lang="en">has_evidence_from_source</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000146 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000146">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000132"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation used to link an assertion or proposition directly to some indicator of the strength of the evidence supporting it.</obo:IAO_0000115>
<rdfs:comment>This is shortcut relation to link an assertion or proposition directly to some indicator of the strength of the evidence supporting it. It is used when there is not enough information to create evidence line(s) for the assertion, but the source provides some indication of the strength of the evidence supporting it.</rdfs:comment>
<rdfs:label xml:lang="en">has_evidence_with_strength</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000150 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000150">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000188"/>
<rdfs:range rdf:resource="http://www.w3.org/ns/prov#Agent"/>
<obo:IAO_0000115>A relation between an entity and an agent who made a contribution to its original creation, or to its subsequent modification, transformation, or assessment.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_contributor</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000151 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000151">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000140"/>
<obo:IAO_0000115>A relation holding between an assertion and an agent that validates its quality - typically by reviewing the provenance and interpretation of evidence on which it is based.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">validity_assessed_by</obo:IAO_0000118>
<rdfs:label>assertion_validated_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000152 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000152">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000140"/>
<rdfs:label xml:lang="en">evidence_strength_assessed_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000159 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000159">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000158"/>
<obo:IAO_0000115>A relation holding between an artifact and a contribution made by a particular agent to its creation, modification, assessment, or destruction.</obo:IAO_0000115>
<obo:IAO_0000116>Consider sup-properties specific to the type of contribuion make, to support property chains for inferring a direct realtiomnship between the artifact/entitiy contributed to, and a related agent or date. At present, we could only support:
- qualified_contribution o date_of_contribution -> dc:date
Want to be able to support inferences such as:
- qualified_creation o date_of_contribution -> date_created
- qualified_evaluation o date_of_contribution -> date_evaluated
- qualified_modification o date_of_contribution -> date_modified</obo:IAO_0000116>
<obo:IAO_0000118>has_contribution</obo:IAO_0000118>
<rdfs:comment>Analogous to PROV qualified Attribution - use to capture additional information about the contribution made by an agent, such as a role they played, or organization on behalf of which the contribution was made.</rdfs:comment>
<rdfs:label xml:lang="en">qualified_contribution</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000167 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000167">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<obo:IAO_0000115>a relation between an assertion and a value that indicates the degree of confidence that the Proposition it puts forth is true.</obo:IAO_0000115>
<obo:IAO_0000118>assertion_trust_rating</obo:IAO_0000118>
<rdfs:comment>Different data sources often create their own scales or value sets to capture this concept. e.g. CIViC 'Trust Ratings' are based on a 5 star system.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_confidence_level</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000169 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000169">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000158"/>
<rdfs:range rdf:resource="http://www.w3.org/ns/prov#Agent"/>
<obo:IAO_0000115>a relation between an agent and an other agent, typically an organization, on whose behalf a Contribution is made.</obo:IAO_0000115>
<rdfs:label xml:lang="en">made_on_behalf_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000178 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000178">
<obo:IAO_0000115>A relation between one entity and an informtion content entity that provides a description of it.</obo:IAO_0000115>
<obo:IAO_0000116>Consider: http://semanticscience.org/resource/SIO_000557 ! 'is described by'</obo:IAO_0000116>
<rdfs:label xml:lang="en">is_described_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000183 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000183">
<obo:IAO_0000115>A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).</obo:IAO_0000115>
<rdfs:label xml:lang="en">evidence direction</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000188 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000188">
<rdfs:comment>A relation between an agent and an entity toward which the agent made a contribution.</rdfs:comment>
<rdfs:label xml:lang="en">contributed_to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000189 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000189">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000173"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation that holds between a statement and a piece of information that supports its validity (i.e. supports its being true).</obo:IAO_0000115>
<rdfs:comment>This relation can be used to link an assertion directly to evidence items that support it. These evidence items are typically organized first into 'evidence lines' that group them according to the argument(s) to which they contribute. But this relation supports use cases where it is desirable to elide over this level of organization and create direct links from an assertion to the fundamental pieces of information that represent evidence supporting it. Note that SEPIO defines a property chain (has_evidence_line o has_evidence_item -> has_supporting_data) that can be used to infer this direct edge, facilitating interoperability between datasets that do and don't implement evidence lines to organize evident items.</rdfs:comment>
<rdfs:label xml:lang="en">has_supporting_data</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000197 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000197">
<obo:IAO_0000115>A relationship that holds between an assertion and a term that summarizes its asserted conclusion.</obo:IAO_0000115>
<obo:IAO_0000118>asserted_outcome</obo:IAO_0000118>
<terms:source>ClinGen (http://datamodel.clinicalgenome.org/interpretation/master/tech/variant_interpretation.html)</terms:source>
<rdfs:label xml:lang="en">asserted_conclusion</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000232 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000232">
<rdfs:label xml:lang="en">has_quantifier</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000255 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000255">
<obo:IAO_0000115>A relation that holds between a statement and a method that was used in generating the statement or any data that supports it.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_supporting_method</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000257 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000257">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000173"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>A relation that holds between a study finding and a data item it describes (i.e. a data item generated by the study whose results are described by the finding).</obo:IAO_0000115>
<obo:IAO_0000118>describes_study_data</obo:IAO_0000118>
<rdfs:label xml:lang="en">describes_data_item</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/dc/terms/source -->
<owl:ObjectProperty rdf:about="http://purl.org/dc/terms/source"/>
<!-- http://purl.org/oban/association_has_object -->
<owl:ObjectProperty rdf:about="http://purl.org/oban/association_has_object">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:label>association has object</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/oban/association_has_predicate -->
<owl:ObjectProperty rdf:about="http://purl.org/oban/association_has_predicate">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_predicate :thing1).
The assertion_has_predicate property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the predicate of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_predicate).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">association has predicate</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/oban/association_has_subject -->
<owl:ObjectProperty rdf:about="http://purl.org/oban/association_has_subject">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:label>association has subject</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/authoredBy -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/authoredBy">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000150"/>
<rdfs:comment>An agent that originated or gave existence to the work that is expressed by the digital resource.
The author of the content of a resource may be different from the creator of the resource representation (although they are often the same). See pav:createdBy for a discussion.
pav:authoredBy is more specific than its superproperty dct:creator - which might or might not be interpreted to also cover the creation of the representation of the artifact.
The author is usually not a software agent (which would be indicated with pav:createdWith, pav:createdBy or pav:importedBy), unless the software actually authored the content itself; for instance an artificial intelligence algorithm which authored a piece of music or a machine learning algorithm that authored a classification of a tumor sample.
The date of authoring can be expressed using pav:authoredOn - note however in the case of multiple authors that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy.</rdfs:comment>
<rdfs:label>Authored by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/createdBy -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/createdBy">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000150"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002353"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000017"/>
</owl:propertyChainAxiom>
<obo:IAO_0000116>SEPIO creates this relation distinct from existing PAV and PROV relations (e.g. pcav:createdBy), which are too specific about whether a relation refers to the agent who created the abstract information content, vs who serialized and documented in concrete form.</obo:IAO_0000116>
<oboInOwl:hasDbXref>http://purl.org/dc/terms/creator</oboInOwl:hasDbXref>
<rdfs:comment>An agent primary responsible for making the digital artifact or resource representation.
This property is distinct from forming the content, which is indicated with pav:contributedBy or its subproperties; pav:authoredBy, which identifies who authored the knowledge expressed by this resource; and pav:curatedBy, which identifies who curated the knowledge into its current form.
pav:createdBy is more specific than its superproperty dct:creator - which might or might not be interpreted to cover this creator.
For instance, the author wrote 'this species has bigger wings than normal' in his log book. The curator, going through the log book and identifying important knowledge, formalizes this as 'locus perculus has wingspan > 0.5m'. The creator enters this knowledge as a digital resource in the knowledge system, thus creating the digital artifact (say as JSON, RDF, XML or HTML).
A different example is a news article. pav:authoredBy indicates the journalist who wrote the article. pav:contributedBy can indicate the artist who added an illustration. pav:curatedBy can indicate the editor who made the article conform to the news paper's style. pav:createdBy can indicate who put the article on the web site.
The software tool used by the creator to make the digital resource (say Protege, Wordpress or OpenOffice) can be indicated with pav:createdWith.
The date the digital resource was created can be indicated with pav:createdOn.
The location the agent was at when creating the digital resource can be made using pav:createdAt.</rdfs:comment>
<rdfs:label xml:lang="en">Created by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/curatedBy -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/curatedBy">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000150"/>
<obo:IAO_0000115>Specifies an agent specialist responsible for shaping the expression in an appropriate format. Often the primary agent responsible for ensuring the quality of the representation.
The curator may be different from the author (pav:authoredBy) and creator of the digital resource (pav:createdBy).
The curator may in some cases be a software agent, for instance text mining software which adds hyperlinks for recognized genome names.
The date of curating can be expressed using pav:curatedOn - note however in the case of multiple curators that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy</obo:IAO_0000115>
<rdfs:label xml:lang="en">Curated by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/derivedFrom -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/derivedFrom">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/source"/>
<rdfs:comment>Derived from a different resource.
Derivation conserns itself with derived knowledge. If this resource has the same content as the other resource, but has simply been transcribed to fit a different model (like XML -> RDF or SQL -> CVS), use pav:importedFrom. If a resource was simply retrieved, use pav:retrievedFrom. If the content has however been further refined or modified, pav:derivedFrom should be used.
Details about who performed the derivation (e.g. who did the refining or modifications) may be indicated with pav:contributedBy and its subproperties.</rdfs:comment>
<rdfs:label>Derived from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/importedFrom -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/importedFrom">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/source"/>
<obo:IAO_0000115>The original source of imported information.
Import means that the content has been preserved, but transcribed somehow, for instance to fit a different representation model by converting formats. Examples of import are when the original was JSON and the current resource is RDF, or where the original was an document scan, and this resource is the plain text found through OCR.
The imported resource does not have to be complete, but should be consistent with the knowledge conveyed by the original resource.
If additional knowledge has been contributed, pav:derivedFrom would be more appropriate.
If the resource has been copied verbatim from the original representation (e.g. downloaded), use pav:retrievedFrom.
To indicate which agent(s) performed the import, use pav:importedBy. Use pav:importedOn to indicate when it happened.</obo:IAO_0000115>
<rdfs:label xml:lang="en">Imported from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/retrievedFrom -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/retrievedFrom">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/source"/>
<rdfs:comment>The URI where a resource has been retrieved from.
The retrieving agent is usually a software entity, which has done the retrieval from the original source without performing any transcription.
Retrieval indicates that this resource has the same representation as the original resource. If the resource has been somewhat transformed, use pav:importedFrom instead.
The time of the retrieval should be indicated using pav:retrievedOn. The agent may be indicated with pav:retrievedBy.</rdfs:comment>
<rdfs:label>Retrieved from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/pav/sourceAccessedAt -->
<owl:ObjectProperty rdf:about="http://purl.org/pav/sourceAccessedAt">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/source"/>
<rdfs:comment>Source accessed at</rdfs:comment>
<rdfs:comment>The resource is related to a given source which was accessed or consulted (but not retrieved, imported or derived from). This access can be detailed with pav:sourceAccessedBy and pav:sourceAccessedOn.
For instance, a curator (pav:curatedBy) might have consulted figures in a published paper to confirm that a dataset was correctly pav:importedFrom the paper's supplementary CSV file.
Another example: I can access the page for tomorrow weather in Boston (http://www.weather.com/weather/tomorrow/Boston+MA+02143) and I can blog ‘tomorrow is going to be nice’. The source does not make any claims about the nice weather, that is my interpretation; therefore the blog post has pav:sourceAccessedAt the weather page.</rdfs:comment>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/ERO_0000480 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/ERO_0000480">
<obo:IAO_0000115>Web address of the resource</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_url</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000021 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000021">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000116>SEPIO creates a relation separate from existing PAV and PROV relations (e.g. pac:createdOn) which are too specific about whether a relation refers to the date on which the abstract information content was created, or when it was serialized and documented in a concrete format.</obo:IAO_0000116>
<obo:IAO_0000118>created_on</obo:IAO_0000118>
<obo:SEPIO_0000052>Consider:
1. http://purl.org/dc/terms/created
2. http://purl.org/pav/createdOn ! Created on
Def: The date of creation of the resource representation. The agents responsible can be indicated with pav:createdBy. This property is normally used in a functional way, indicating the time of creation, although PAV does not formally restrict this. pav:lastUpdateOn can be used to indicate minor updates that did not affect the creating date.
3. prov:generatedAtTime: The time at which an entity was completely created and is available for use.</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">date_created</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000036 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000036">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000115>The most recent data on which an entity was modified or updated.</obo:IAO_0000115>
<obo:IAO_0000118>date_last_updated</obo:IAO_0000118>
<obo:SEPIO_0000052>http://purl.org/dc/terms/modified ! Date Modified
Definition: Date on which the resource was changed.</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">date_modified</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000040 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000040">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:label xml:lang="en">date_evaluated</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000051 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000051">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:SEPIO_0000052>http://purl.org/dc/terms/dateSubmitted</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">date_submitted</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000063 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000063">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000160"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000116>Consider: http://www.w3.org/ns/prov#startedAtTime</obo:IAO_0000116>
<rdfs:label xml:lang="en">date_started</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000105 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000105">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<rdfs:label xml:lang="en">date_created_before</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000123 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000123">
<rdfs:comment>Relation between a report and a string of text that it contains</rdfs:comment>
<rdfs:label xml:lang="en">has_textual_part</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000135 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000135">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000021"/>
<obo:IAO_0000115>A relation holding between an assertion and the date on which it was asserted.</obo:IAO_0000115>
<obo:IAO_0000118>asserted_on</obo:IAO_0000118>
<rdfs:label xml:lang="en">date_asserted</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000141 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000141">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000040"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<obo:IAO_0000118>evidence_assessed_on</obo:IAO_0000118>
<rdfs:label xml:lang="en">date_evidence_strength_assessed</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000160 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000160">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#dateTime"/>
<obo:IAO_0000118>time_of_activity</obo:IAO_0000118>
<rdfs:label xml:lang="en">date_of_activity</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000161 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000161">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000160"/>
<obo:IAO_0000116>Consider: http://www.w3.org/ns/prov#endedAtTime</obo:IAO_0000116>
<rdfs:label xml:lang="en">date_ended</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000162 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000162">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<obo:IAO_0000116>Consider: http://purl.org/pav/curatedOn
Definition: The date this resource was curated.
pav:curatedBy gives the agent(s) that performed the curation.
This property is normally used in a functional way, indicating the last curation date, although PAV does not formally restrict this.
The value is of type xsd:dateTime, for instance "2013-03-26T14:49:00+01:00"^^xsd:dateTime. The timezone information (Z for UTC, +01:00 for UTC+1, etc) SHOULD be included unless unknown. If the time (or parts of time) is unknown, use 00:00:00Z. If the day/month is unknown, use 01-01, for instance, if we only know September 1983, then use "1983-09-01T00:00:00Z"^^xsd:dateTime.</obo:IAO_0000116>
<rdfs:label xml:lang="en">date_curated</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000163 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000163">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000160"/>
<rdfs:label xml:lang="en">date_of_contribution</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000164 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000164">
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/date"/>
<obo:IAO_0000116>Consider: http://purl.org/pav/lastUpdateOn</obo:IAO_0000116>
<rdfs:label xml:lang="en">date_updated</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000165 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000165">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000040"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<obo:IAO_0000115>A relation holding between an artifact (e.g. an asseriton) and the date/time at which it was validated as meeting some standard of quality or rigor.</obo:IAO_0000115>
<rdfs:label xml:lang="en">date_validated</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000168 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000168">
<obo:IAO_0000115>A quantitative value that can be interpreted as an indicator of the degree of confidence that the Proposition put forth by an Assertion is true.</obo:IAO_0000115>
<obo:IAO_0000116>This property has a similar intent as assertion_confidence_level, but used for quantitative numerical values.</obo:IAO_0000116>
<rdfs:comment>The 'assertion confidence score' property does not only include statistical measures such as p-values that explicitly indicate a level of confidence,. It also includes any quantitative score against which a threshold for making an assertion is defined - where the distance of this score from this threshold can be interpreted as an indicator of how much confidence we might have that the asserted conclusion is true.
For example, many silico prediction tools such as SIFT interogate biological sequence data to calculate a score that reflects the likelihood that a particular sequence variant negatively impacts gene product function. A variant is interpreted to be 'Tolerated', 'Damaging', or 'Deleterious' based on how its score compares against pre-defined thresholds. Here, we may have less confidence that a variant with a score just above the 'Damaging' threshold is truly damaging, versus a variant whose score is well above the threshold.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_confidence_score</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000231 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000231">
<rdfs:label xml:lang="en">quantifier</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000129 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000129">
<obo:SEPIO_0000052>http://www.w3.org/ns/prov#value
'This property serves the same purpose as rdf:value, but has been reintroduced to avoid some of the definitional ambiguity in the RDF specification (specifically, 'may be used in describing structured values'). The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue'</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">has_value</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/dc/elements/1.1/description -->
<owl:DatatypeProperty rdf:about="http://purl.org/dc/elements/1.1/description">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<obo:IAO_0000115>An account of a resource.</obo:IAO_0000115>
<rdfs:label>description</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/dc/terms/date -->
<owl:DatatypeProperty rdf:about="http://purl.org/dc/terms/date">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#dateTime"/>
<obo:IAO_0000115>A point or period of time associated with an event in the lifecycle of the resource.</obo:IAO_0000115>
<obo:IAO_0000116>Consider: http://purl.org/pav/contributedOn</obo:IAO_0000116>
<rdfs:label xml:lang="en">date</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/dc/terms/identifier -->
<owl:DatatypeProperty rdf:about="http://purl.org/dc/terms/identifier">
<rdfs:label xml:lang="en">identifier</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.org/pav/version -->
<owl:DatatypeProperty rdf:about="http://purl.org/pav/version">
<rdfs:comment>The version number of a resource. This is a freetext string, typical values are "1.5" or "21". The URI identifying the previous version can be provided using prov:previousVersion.
This property is normally used in a functional way, although PAV does not formally restrict this.</rdfs:comment>
<rdfs:label>version</rdfs:label>
</owl:DatatypeProperty>
<!-- http://xmlns.com/foaf/0.1/name -->
<owl:DatatypeProperty rdf:about="http://xmlns.com/foaf/0.1/name">
<obo:IAO_0000115>A name for some thing.</obo:IAO_0000115>
<rdfs:label>name</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<obo:BFO_0000179>entity</obo:BFO_0000179>
<obo:BFO_0000180>Entity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Julius Caesar</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">Verdi’s Requiem</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the Second World War</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your body mass index</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">entity</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget xml:lang="en">Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000004"/>
<rdfs:comment>per discussion with Barry Smith</rdfs:comment>
<rdfs:seeAlso rdf:resource="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/001-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:BFO_0000179>continuant</obo:BFO_0000179>
<obo:BFO_0000180>Continuant</obo:BFO_0000180>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget xml:lang="en">Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000007"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/008-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/126-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/009-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/011-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/009-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/126-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/008-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/011-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<obo:BFO_0000179>occurrent</obo:BFO_0000179>
<obo:BFO_0000180>Occurrent</obo:BFO_0000180>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.</obo:IAO_0000116>
<obo:IAO_0000116>Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">occurrent</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget xml:lang="en">Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000006"/>
<rdfs:comment>per discussion with Barry Smith</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget>Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000012"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/077-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/108-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/079-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/108-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/079-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:BFO_0000179>ic</obo:BFO_0000179>
<obo:BFO_0000180>IndependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a chair</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a leg</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a molecule</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a spatial region</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an atom</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an orchestra.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the bottom right portion of a human torso</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your mouth</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])</obo:IAO_0000115>
<obo:IAO_0000601 xml:lang="en">For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] </obo:IAO_0000602>
<obo:IAO_0000602>(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">independent continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/134-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/018-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/134-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/018-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:BFO_0000179>process</obo:BFO_0000179>
<obo:BFO_0000180>Process</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a process of cell-division, \ a beating of the heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a process of meiosis</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a process of sleeping</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the course of a disease</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the flight of a bird</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the life of an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your process of aging.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)</obo:IAO_0000116>
<obo:IAO_0000602>(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">process</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/083-003"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/083-003"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:BFO_0000179>disposition</obo:BFO_0000179>
<obo:BFO_0000180>Disposition</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">an atom of element X has the disposition to decay to an atom of element Y</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">certain people have a predisposition to colon cancer</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">children are innately disposed to categorize objects in certain ways.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the cell wall is disposed to filter chemicals in endocytosis and exocytosis</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">disposition</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/062-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/063-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/063-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/062-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:BFO_0000179>realizable</obo:BFO_0000179>
<obo:BFO_0000180>RealizableEntity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the disposition of this piece of metal to conduct electricity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of your blood to coagulate</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of your reproductive organs</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of this boundary to delineate where Utah and Colorado meet</obo:IAO_0000112>
<obo:IAO_0000600 xml:lang="en">To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">realizable entity</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/058-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/060-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/060-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/058-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:BFO_0000179>quality</obo:BFO_0000179>
<obo:BFO_0000180>Quality</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the ambient temperature of this portion of air</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the color of a tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the length of the circumference of your waist</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mass of this piece of gold.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of your nose</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of your nostril</obo:IAO_0000112>
<obo:IAO_0000600 xml:lang="en">a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">quality</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/055-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/105-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/055-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/105-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>sdc</obo:BFO_0000179>
<obo:BFO_0000180>SpecificallyDependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of one-sided specifically dependent continuants: the mass of this tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of this fish to decay</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of this heart: to pump blood</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of proton donors and acceptors in chemical reactions [79</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pink color of a medium rare piece of grilled filet mignon at its center</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of this hole.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the smell of this portion of mozzarella</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.</obo:IAO_0000116>
<obo:IAO_0000602>(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
<owl:annotatedTarget xml:lang="en">Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000005"/>
<rdfs:comment>per discussion with Barry Smith</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:BFO_0000179>role</obo:BFO_0000179>
<obo:BFO_0000180>Role</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the priest role</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a boundary to demarcate two neighboring administrative territories</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a building in serving as a military target</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a stone in marking a property boundary</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of subject in a clinical trial</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the student role</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">role</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/061-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/061-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>gdc</obo:BFO_0000179>
<obo:BFO_0000180>GenericallyDependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pdf file on your laptop, the pdf file that is a copy thereof on my laptop</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</obo:IAO_0000115>
<obo:IAO_0000602>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">generically dependent continuant</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/074-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/074-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:BFO_0000179>function</obo:BFO_0000179>
<obo:BFO_0000180>Function</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the function of a hammer to drive in nails</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of a heart pacemaker to regulate the beating of a heart through electricity</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of amylase in saliva to break down starch into sugar</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">function</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/064-001"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/064-001"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<obo:BFO_0000179>material</obo:BFO_0000179>
<obo:BFO_0000180>MaterialEntity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a flame</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a forest fire</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a human being</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a hurricane</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a photon</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a puff of smoke</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a sea wave</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a tornado</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an aggregate of human beings.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an energy wave</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an epidemic</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the undetached arm of a human being</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">material entity</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/019-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/020-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
<owl:annotatedTarget xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/021-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/019-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/021-002"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
<owl:annotatedTarget>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] </owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/020-002"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:BFO_0000179>immaterial</obo:BFO_0000179>
<obo:BFO_0000180>ImmaterialEntity</obo:BFO_0000180>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10</obo:IAO_0000116>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">immaterial entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000182 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000182">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:comment>A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])</rdfs:comment>
<rdfs:label>history</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0001716 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0001716">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>A database is an organized collection of data, today typically in digital form.</obo:IAO_0000115>
<oboInOwl:hasDbXref>http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Database</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">database</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000009">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label</obo:IAO_0000115>
<obo:IAO_0000232>9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.</obo:IAO_0000232>
<rdfs:label>datum label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000311"/>
<obo:IAO_0000111 xml:lang="en">journal article</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a report that is published in a journal</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000159</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">journal article</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">data item</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Data items include counts of things, analyte concentrations, and statistical summaries.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.</obo:IAO_0000116>
<obo:IAO_0000116>2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Jonathan Rees</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">data</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data item</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A generically dependent continuant that is about some thing.</obo:IAO_0000115>
<rdfs:label xml:lang="en">information content entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">directive information entity</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An information content entity whose concretizations indicate to their bearer how to realize them in a process.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">directive information entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000064 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000064">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000115>A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.</obo:IAO_0000115>
<rdfs:label>algorithm</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000088 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000088">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<obo:IAO_0000111 xml:lang="en">report</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification</obo:IAO_0000116>
<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_0000117 xml:lang="en">PERSON:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP: OBI</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">OBI_0000099</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">report</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000100 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000100">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">data set</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type</obo:IAO_0000116>
<obo:IAO_0000116>2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Allyson Lister</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000042</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000109 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000109">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">measurement datum</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2/2/2009 is_specified_output of some assay?</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000305</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000306 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000306">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions</obo:IAO_0000115>
<rdfs:label>table</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000308 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000308">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">figure</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Any picture, diagram or table</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">figure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000310 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000310">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">document</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A journal article, patent application, laboratory notebook, or a book</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A collection of information content entities intended to be understood together as a whole</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">document</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000311 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000311">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<obo:IAO_0000111 xml:lang="en">publication</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A journal article or book</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A document that has been accepted by a publisher</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">publication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000313 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000313">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<obo:IAO_0000111 xml:lang="en">patent</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">US Patent 6,449,603</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A document that has been accepted by a patent authority</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">patent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OAE_0001563 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OAE_0001563">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:label xml:lang="en">proportional reporting ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011">
<rdfs:subClassOf rdf:resource="http://www.w3.org/ns/prov#Activity"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000017"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/ns/prov#Agent"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">planned process</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Injecting mice with a vaccine in order to test its efficacy</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A processual entity that realizes a plan which is the concretization of a plan specification.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">branch derived</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">6/11/9: Edited at workshop. Used to include: is initiated by an agent</obo:IAO_0000232>
<obo:IAO_0000232 xml:lang="en">This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">planned process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000066 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000066">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000004"/>
<obo:IAO_0000115>a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).</obo:IAO_0000115>
<rdfs:label xml:lang="en">investigation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000070 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000070">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000004"/>
<rdfs:label xml:lang="en">assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000175 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000175">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000111 xml:lang="en">p-value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000121"/>
<obo:IAO_0000115 xml:lang="en">A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">May be outside the scope of OBI long term, is needed so is retained</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WEB: http://en.wikipedia.org/wiki/P-value</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">p-value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000181 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000181">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000000"/>
<obo:IAO_0000115>a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area</obo:IAO_0000115>
<rdfs:label>population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000235 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000235">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000111 xml:lang="en">standard error</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group:OBI</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">see P-Value</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">standard error</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000338 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000338">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000003"/>
<obo:IAO_0000111 xml:lang="en">drawing a conclusion based on data</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">drawing a conclusion based on data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000938 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000938">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<obo:IAO_0000115>A measurement datum that is reported on a categorical scale</obo:IAO_0000115>
<rdfs:label>categorical measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000963 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000963">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000009"/>
<obo:IAO_0000112>The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.</obo:IAO_0000112>
<obo:IAO_0000115>A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.</obo:IAO_0000115>
<rdfs:label>categorical label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001146 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001146">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">binding assay</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An assay with the objective to characterize the disposition of two or more material entities to form a complex.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">binding assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001442 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001442">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">q-value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000117 xml:lang="en">PERS:Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">FDR adjusted p-value</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">q-value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001930 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001930">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<obo:IAO_0000115>A value specification that is specifies one category out of a fixed number of nominal categories</obo:IAO_0000115>
<rdfs:label>categorical value specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001933 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001933">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>An information content entity that specifies a value within a classification scheme or on a quantitative scale.</obo:IAO_0000115>
<obo:IAO_0000116>This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.</obo:IAO_0000116>
<rdfs:label>value specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0002165 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002165">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein localization assay</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca Tauber</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI development call</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein localization assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0302840 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302840">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">curated information</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions.</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">curated information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>A material entity that consists of two or more organisms, viruses, or viroids.</obo:IAO_0000115>
<rdfs:label>collection of organisms</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000000"/>
<obo:IAO_0000115>A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.</obo:IAO_0000115>
<rdfs:label>family</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<obo:IAO_0000112>The proposition that BRCA1:2685T>A causes familial breast cancer.</obo:IAO_0000112>
<obo:IAO_0000115>An abstract entity representing the sharable meaning of what is expressed in a particular assertion.</obo:IAO_0000115>
<obo:IAO_0000116>In the SEPIO model, an assertion is akin to an act in speech or text that expresses beleif in the truth of a proposition. It is the proposition that represents the semantic content of a claim, and bears truth value.
Mappings to terms from related models:
1. http://purl.org/see/rdo#proposition
A SEPIO proposition is equivalent to a 'proposition' from the Semantic EvidencE framework. "The class rdo:proposition represents propositions i.e. the sharable objects of propositional attitudes like belief or desire and the bearers of truth values. As truth bearers they are either true or false. They are taken to represent the semantic content of sentences or larger lexical entities formulated in some natural or artificial language.")
2. http://purl.org/mp/Holotype
The notion of a holotype from the Micropublications model is related to a SPEIO proposition - in that it represents a statement that is selcted to all other statements expressing the same meaning.
3. http://purl.org/oban/association
An OBAN proposition is a more type of proposition, that is structured/expressed according to the specifications laid out in the OBAN ontology.</obo:IAO_0000116>
<obo:IAO_0000119>http://plato.stanford.edu/entries/propositions</obo:IAO_0000119>
<rdfs:comment>The notion of a proposition, and its relationship to an assertion, derives from the domain of logic and philosophy [12]. Propositions are abstract entities that, like numbers, are independent of space and time. They represent only the meaning that is expressed in a particular agent’s assertion, and are ‘sharable’ in that the same proposition can be expressed in many different assertions. Propositions are primary bearers of truth value, in that they are true or false.
From http://plato.stanford.edu/entries/propositions/: "Propositions are the sharable objects of the attitudes and the primary bearers of truth and falsity. This stipulation rules out certain candidates for propositions, including thought- and utterance-tokens, which presumably are not sharable, and concrete events or facts, which presumably cannot be false."</rdfs:comment>
<rdfs:label xml:lang="en">proposition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002353"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000003"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000130"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/ns/prov#Agent"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000135"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#dateTime"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The following are three seperate assertion instances, that assert the same proposition (that BRCA1:2685T>A causes familial breast cancer)
1. Counsyl's assertion on October 5, 2009 that BRCA1:2685T>A causes familial breast cancer.
2. The ENIGMA consortium’s assertion on September 18, 2010 that BRCA1:2685T>A causes familial breast cancer.
3. A later assertion by the ENIGMA consortium on May 9, 2013, based on new evidence, that BRCA1:2685T>A causes familial breast cancer.</obo:IAO_0000112>
<obo:IAO_0000115>An information content entity representing a statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence.</obo:IAO_0000115>
<obo:IAO_0000116>In SEPIO, a high-level distinction is made between Statements that are 'Findings' vs 'Assertions'. Findings are statements that report what was observed in an experiment or study, and are about only the direct participants in the experiment or study. Assertions are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence', and often make broader claims about the types or categories to which study participants belong.
This distinction is important because the provenance and validity of a finding does not depend on evidence in the same way that of an assertion does. This has modeling implications for findings and assertions are linked to information that supports them.</obo:IAO_0000116>
<obo:IAO_0000118>claim</obo:IAO_0000118>
<obo:IAO_0000118>evidence-based assertion</obo:IAO_0000118>
<obo:IAO_0000118>propostional assertion</obo:IAO_0000118>
<obo:IAO_0000119>Derived from http://purl.org/see/rdo#assertion</obo:IAO_0000119>
<obo:SEPIO_0000184>The identity of a particular assertion is dependent upon (1) what it claims to be true (its semantic content, aka its ‘proposition’), (2) the agent asserting it, and (3) the occasion on which the assertion is made. Many agents can make assertions expressing belief in the same proposition (e.g. ENIGMA’s assertion that that BRCA1:2685T>A causes familial breast cancer is a separate instance than Counsyl’s assertion of the same underlying proposition). Likewise, a single agent can make more than one assertion of belief in the same proposition on different occasions (e.g. ENIGMA may make a separate assertion of the same proposition that BRCA1:2685T>A causes familial breast cancer at a later date, based on additional evidence).</obo:SEPIO_0000184>
<rdfs:comment>Assertions as defined in SEPIO are the result of some logical inference made based on the interpretation of evidence. They put forth a proposition that may or may not be true. The validity of this proposition ultimately rests on the quantity, quality, diversity, and concordance of evidence supporting it.
Statements directly reporting study outcomes or findings are not considered assertions in this sense, as they merely report what was observed or recorded, but do not rely on a leap of logical inference (see 'study finding').</rdfs:comment>
<rdfs:label xml:lang="en">assertion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000149"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>An example of an evidence line would be the argument that a finding such as "Lepr1 KO mice exhibit lower blood glucose levels than matched WT controls" makes in support of the proposition that "Lepr1 gene is involved in diabetes". The Evidence Items supporting this line of evidence could include experimental data from a study exploring blood glucose levels in Lepr1 KO mice, such as a 548.5 mg/dl measurement of blood glucose in a Lepr<tm1b/tm1b> mutant mouse, or a 1.3951e-24 p-value indicating this measure to be significantly different from wild-type mice.
Here, the finding and its supporting data exist independently of their use as evidence. An Evidence Line instance based on this finding comes into existence only when an agent interprets this it as an independently meaningful argument for a particular Proposition, in the act of making an Assertion.
(This example is based on data from the IMPC record here: http://bit.ly/2t4J1TI)</obo:IAO_0000112>
<obo:IAO_0000115>An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence.</obo:IAO_0000115>
<rdfs:comment>An evidence line is created through the interpretation of one or more pieces of information that collectively support a meaningful argument for or against a proposition. To qualify as an Evidence Line, this argument must be independently significant as evidence - i.e. it must be capable of affecting the probability of accepting the target proposition as true. This does not mean, however, that it is independently sufficient to establish belief in the proposition, as additional evidence lines may be required to ultimately accept the proposition as true.
For example, in the ACMG framework for variant interpretations establishes "absence in population databases" as a type of evidence line that can argue for the pathogenicty of a particular variant. But this argument alone is not considered sufficient to establish a variant's pathogencity, as the other types of evidence are additionally required to establish the truth of this Proposition (e.g. a line of evidence demonstrating the variant to have a deleterious effect on protein function, or showing it to segregate with disease features in a family tree).</rdfs:comment>
<rdfs:label xml:lang="en">evidence line</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002233"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002234"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An act of interpreting evidence to make an assertion of belief that a particular proposition is true</obo:IAO_0000115>
<obo:IAO_0000116>Mappings to terms from related models:
Likely equivalent to http://purl.org/see/rdo#act_of_inference.
May be equivalent to http://purl.obolibrary.org/obo/ECO_0000217 ! assertion method.</obo:IAO_0000116>
<obo:IAO_0000118>act of assertion</obo:IAO_0000118>
<rdfs:comment>An assertion process includes the processes of interpreting data and evaluating it as evidence for the validity of a proposition. They are affected by a particular agents on a particular occasions, and can be specified by assertion methods or guidelines.</rdfs:comment>
<rdfs:label xml:lang="en">assertion process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002234"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A planned process executed in the performance of scientific research wherein systematic investigations are performed to establish facts and reach new conclusions about phenomena in the world.</obo:IAO_0000115>
<rdfs:comment>Data generation process are typically experimental studies or observations, but can include any process generating information used to evaluate a claim. This is an organizational class that groups more specific types of such processes that are most commonly used in generating data used as evidence to support claims. These processes produce informational artifacts such as measured data values, derived statistical calculations and confidence measures, or statements representing summaries or conclusions drawn from such data.</rdfs:comment>
<rdfs:label xml:lang="en">research activity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000037 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000037">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000115>A directive information entity that specifies an algorithm or heuristics for evaluating evidence in the process of making an assertion.</obo:IAO_0000115>
<obo:IAO_0000116>SEPIO implements several OWL individuals representing instances of commonly applied assertion methods, primarily those used in pathogenic variant classification such as the ACMG variant classification criteria.</obo:IAO_0000116>
<rdfs:comment>Assertion methods can be informal guidlines or heuristics that support manual evaluation of evidence, e.g. the ACMG Variant Classification Guidelines. Assertion methods can also be formally encoded as algorithms that allow computational or statistical analysis of data as evidence in support of making an assertion - e.g. multifactorial analysis algorithms that operate on specified data to generate a quantitative score indicating the validity of a particular proposition.</rdfs:comment>
<rdfs:label xml:lang="en">assertion method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000048 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000048">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000115>A role borne by a person, group, organization, or information processing entity (e.g. software, algorithms) in virtue of its active participation in a process lerading to some outcome (e.g the generation, modification, or provision of some entity).</obo:IAO_0000115>
<obo:SEPIO_0000052>http://purl.org/see/rdo#agent_role</obo:SEPIO_0000052>
<rdfs:comment>In the context of evidence and proveannce, agents are persons, groups, organizations, or software that are responsible for making assertions or generating the evidence and data that support them.</rdfs:comment>
<rdfs:label xml:lang="en">agent role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000049 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000115>A role inhering in any material or information artifact that is used by an agent as specified input into a planned process.</obo:IAO_0000115>
<rdfs:comment>In the context of evidence and provenance for scientific claims, resources are entities that are used by agents to facilitate processes aimed at the generation of assertions or the evidence and data that support them. Examples include instruments, reagents, model systems, software, and protocols.</rdfs:comment>
<rdfs:label xml:lang="en">resource role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000055 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000055">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000129"/>
<obo:IAO_0000116>Mappings to related terms:
1. http://purl.obolibrary.org/obo/ECO_0000218 ! manual assertion
ECO Definition/Comment: A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.</obo:IAO_0000116>
<rdfs:label xml:lang="en">obsolete_manual assertion process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000056 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000056">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000129"/>
<obo:IAO_0000115>An assertion process performed through algorithmic analysis by a computational agent, independent of human review.</obo:IAO_0000115>
<obo:IAO_0000116>Mappings to related terms:
1. http://purl.obolibrary.org/obo/ECO_0000203 ! automatic assertion
ECO Definition/Comment: An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.</obo:IAO_0000116>
<rdfs:comment>Ultimately even automated assertions require a human agent to set a confidence threshhold that determines when a computational output (e.g. a sequence similarity p-value) justifies an assesrtion being made.</rdfs:comment>
<rdfs:label xml:lang="en">obsolete_automated assertion process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000058 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000058">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000182"/>
<obo:IAO_0000115>The process history leading to the creation and current condition of an artifact.</obo:IAO_0000115>
<obo:IAO_0000116>Consider whether it is appropriate to place this under the BFO:history class, which may apply only to histories of "material entities or sites". And consider if we want.need to define this class at all - as it is not used to model data - only as a means to record what SEPIO consider proovenance to be and how it is different from evidence.</obo:IAO_0000116>
<rdfs:comment>For scientific assertions/claims, this is the process history leading to the asseertion being made, including processes through which evidence is evaluated, and processes through which information used as evidence is created. The transitive nature of provenance means that the provenance history of informtion used as supporting data becomes provenance for an assertion that uses this information as evidence. Provenance metadata describes these processes, including accounts of who conducted these processes, what entities participated in them, and when/where they occurred.</rdfs:comment>
<rdfs:label xml:lang="en">provenance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000066 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000066">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000125"/>
<obo:IAO_0000115>A study that involves primary research of subjects or specimens in a natural, cliniclal, or laboratory setting.</obo:IAO_0000115>
<rdfs:label xml:lang="en">primary research study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000067 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000067">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000066"/>
<obo:IAO_0000115>Formal clinical study performed using cohorts of multiple patients</obo:IAO_0000115>
<rdfs:label xml:lang="en">clinical study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000069 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000069">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000067"/>
<obo:SEPIO_0000052>http://purl.org/net/OCRe/research.owl#Interventional_study</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">interventional clinical study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000070 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000070">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000067"/>
<obo:SEPIO_0000052>http://purl.org/net/OCRe/research.owl#Observational_study</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">observational clinical study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000071 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000071">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000070"/>
<obo:SEPIO_0000052>http://purl.org/net/OCRe/research.owl#Case_control_study</obo:SEPIO_0000052>
<rdfs:label xml:lang="en">case-control clinical study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000072 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000072">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000066"/>
<obo:IAO_0000115>A research dtudy perfomred using an experimental model system such as a cell line, or model organism.</obo:IAO_0000115>
<rdfs:label xml:lang="en">experimental model study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000073 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000073">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000072"/>
<rdfs:label xml:lang="en">in vitro study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000074 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000074">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000072"/>
<rdfs:label xml:lang="en">in vivo study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000076 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000076">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000074"/>
<rdfs:label xml:lang="en">cell-based in vivo study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000077 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000077">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000074"/>
<rdfs:label xml:lang="en">tissue-based in vivo study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000078">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000074"/>
<obo:IAO_0000118>whole organism in vivo study</obo:IAO_0000118>
<rdfs:label xml:lang="en">organism-based in vivo study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000079 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000079">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000125"/>
<obo:IAO_0000115>A study based only on analysis of existing data, as found in artifacts such as community/curated databases, raw datasets, or publications.</obo:IAO_0000115>
<obo:IAO_0000118>data-driven study</obo:IAO_0000118>
<rdfs:label xml:lang="en">secondary research study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000080 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000080">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000079"/>
<obo:IAO_0000115>A curation-based study that uses only one or more literature publication as input data source.</obo:IAO_0000115>
<obo:IAO_0000116>Based on ClinVar 'literature only' collection method: "for submissions that provide the interpretation of a variant from one or more publications. No additional curation has been performed by the submitter; the interpretation is from the publication(s) only."</obo:IAO_0000116>
<rdfs:label xml:lang="en">literature-based study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000081 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000081">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000079"/>
<obo:IAO_0000116>Based on Clinvar 'curation' collection method: "for variants that were not directly observed by the submitter, but were interpreted by curation of multiple sources, including clinical testing laboratory reports, publications, private case data, and public databases."</obo:IAO_0000116>
<rdfs:label xml:lang="en">curation-based study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000102 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000102">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000079"/>
<obo:IAO_0000115>A study based on analysis of data gathered from baseline studies of a population group of apparently unaffected individuals to assess allele frequencies</obo:IAO_0000115>
<obo:IAO_0000119>ClinVar</obo:IAO_0000119>
<rdfs:label xml:lang="en">reference population data study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000125 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000125">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000004"/>
<obo:IAO_0000115>A planned proccess that executes some study design or protocol to generate scientific data that is interpreted to test or generate a hypothesis.</obo:IAO_0000115>
<rdfs:label xml:lang="en">research study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000127 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000127">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000129"/>
<obo:IAO_0000115>A group of individuals (organisms, specimens, samples) that are subjects in an observational or intervention study, and whose members represent experimental replicates as defined in a study design by the same independent variable specifications (i.e. subjected to the same selction criteria or set of experimental interventions).</obo:IAO_0000115>
<obo:IAO_0000116>Consider: STATO_0000193, OBI_0000174</obo:IAO_0000116>
<rdfs:label xml:lang="en">obsolete_study group</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000129 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000129">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<rdfs:label xml:lang="en">DeprecatedClass</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000131 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000131">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000004"/>
<obo:IAO_0000115>A planned process in which existing data is collected, organized, and improved in preparation for subsequent use.</obo:IAO_0000115>
<rdfs:label xml:lang="en">curation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000133 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000133">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000179"/>
<obo:IAO_0000115>A categorical value indicating the degree of support an agent believes an evidence line to provide for a particular proposition.</obo:IAO_0000115>
<rdfs:label xml:lang="en">evidence strength level</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000143 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000143">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000066"/>
<obo:IAO_0000115>A study that documents observations or findings from a single patent.</obo:IAO_0000115>
<obo:IAO_0000118>case reporting</obo:IAO_0000118>
<rdfs:label>patient case study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000148 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000148">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:label xml:lang="en">evidence role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000149 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000149">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"/>
<owl:Restriction>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000148"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>- the raw count data from a case-control study comparing the frequency of an allele in two cohorts or populations
- the calculated p-value as a measure of statistical significance of the difference identified in the study
- a published figure documenting these data
- an author statement summarizing the outcomes of the study (i.e. a 'study finding')
- a broader conclusion inferred from interpretation of the data reported in a study (i.e. an evidence-based 'assertion')</obo:IAO_0000112>
<obo:IAO_0000115>An information content entity that is used as evidence to evaluate the validity of a target assertion or proposition.</obo:IAO_0000115>
<obo:IAO_0000118>evidence</obo:IAO_0000118>
<obo:IAO_0000118>evidence information</obo:IAO_0000118>
<rdfs:comment>'Evidence Item' is a broad term covering any information interpreted as evidence in the act of making an assertion.
Classes representing different types of evidence items are imported here from ontologies such as OBI, IAO, and STATO, and include:
- measured data values
- derived data values such as statistical calculations and confidence measures
- figures presenting or describing such data
- author statements representing summaries of or conclusions drawn from such data
- established facts in a field of research
Note that publications and reports are considered separately from 'evidence items', as a they *contain* information (data values, figures author statements) that can be used as evidence. But on its own a publication or report is merely a proxy for this information.</rdfs:comment>
<rdfs:label xml:lang="en">evidence item</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000153 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000153">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
<rdfs:label xml:lang="en">creator role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000154 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000154">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
<rdfs:label xml:lang="en">assessor role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000155 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000155">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000154"/>
<obo:IAO_0000118>validator role</obo:IAO_0000118>
<rdfs:label xml:lang="en">approver role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000156 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000156">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
<rdfs:label xml:lang="en">curator role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000157 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000157">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An autonomous computer program that carries out tasks on behalf of users.</obo:IAO_0000115>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Software_agent</obo:IAO_0000119>
<rdfs:comment>Software agents are designed to execute algorithm(s) that receive some input information and direct its processing to achieve a specified goal.</rdfs:comment>
<rdfs:label xml:lang="en">software agent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000158 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000158">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000163"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#dateTime"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>The actions taken by a particular agent in the creation, modification, assessment, or descruction of an artifact.</obo:IAO_0000115>
<obo:IAO_0000116>This concept is similar in meaning and usage to PROV:Attribution. Consider aligning or adopting.</obo:IAO_0000116>
<rdfs:comment>A contribution describes the part played by a particular agent in the creation, modification, assessment, or descruction of an artifact. The scope of a given 'contribution' instance is constrained to include only the actions of a particular agent in contributing to a particular artifact. Contribution instances are used to organize information about when, where, how (e.g. what roles were played), and on whose behalf these actions were performed.</rdfs:comment>
<rdfs:label xml:lang="en">contribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000173 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000173">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
<obo:IAO_0000112>A statement summarizing the outcome of a sequencing analysis: "Sequencing of DNA from patient X revealed an A->T mutation at position 2143 in gene Y".
A statement summarizing the outcome of a variant population frequency study: "The frequency of variant X is 0.00015 in a cohort of non-finnish european subjects described in the ExAC dataset."</obo:IAO_0000112>
<obo:IAO_0000115>A statement about the outcome of a scientific experiment or study, describing what an agent observed, what a device recorded, or mathematical calculations derived.</obo:IAO_0000115>
<obo:IAO_0000118>experimental finding</obo:IAO_0000118>
<obo:IAO_0000118>study outcome</obo:IAO_0000118>
<rdfs:comment>An experimental finding is a statement that summarizes the direct outcomes of a particular experiment or study. It describes only what was observed, recorded, or calculated, and not more general conclusions that may have been inferred from such findings. As such, the scope of what a finding is about is limited to the direct participants in the study - i.e. it describes only the instances observed or recorded in the study. It makes no broader inference or conclusion about types or classes to which these instances belong.
This does not mean that the observations were necessarily accurate or correct - only that they were indeed made in a particular study. For example, the finding that "Sequencing of DNA from patient X revealed an A->T mutation at position 2143 in gene Y" is a matter of fact, even if the finding is an artifact of an erroneous sequence read, or the sequencing coverage is so low that this finding may be wrong. Metadata about the finding, such as sequencing methods used, coverage or read depth, are recoded so users can judge for themselves whether the objectively reported finding accurtely reflects the biology it describes.</rdfs:comment>
<rdfs:comment>In SEPIO, a high-level distinction is made between Statements that are 'Findings' vs 'Assertions'. Findings are statements that report what was observed in an experiment or study, and are about only the direct participants in the experiment or study. Assertions are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence', and often make broader claims about the types or categories to which study participants belong.
This distinction is important because the provenance and validity of a finding does not depend on evidence in the same way that of an assertion does. This has modeling implications for findings and assertions are linked to information that supports them.</rdfs:comment>
<rdfs:label xml:lang="en">study finding</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000174 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000112>The following is derived from https://en.wikipedia.org/wiki/Statement_(logic):
Examples of sentences that are (or make) statements:
"Socrates is a man."
"A triangle has three sides."
"Madrid is the capital of Spain."
"There are five ducks on the lake"
"The BRAF V600E mutation causes breast cancer"
Examples of sentences that are not (or do not make) statements:
"Who are you?"
"Run!"
"Greenness perambulates."
"I had one grunch but the eggplant over there."
"The King of France is wise."
"Broccoli tastes good."
The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste.</obo:IAO_0000112>
<obo:IAO_0000115>An information content entity expressing a declarative sentence that is either true or false.</obo:IAO_0000115>
<rdfs:comment>From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21):
"A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities."
----
Note that the definition in (b) describes the notion of a 'Proposition' as defined in SEPIO, such that Propositions are classified as a type of Statement.</rdfs:comment>
<rdfs:comment>Statements are sentences that declare a definitive or proposed facts - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made.
The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth.</rdfs:comment>
<rdfs:label xml:lang="en">statement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000175 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000175">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000129"/>
<obo:IAO_0000115>A statement describing something that was observed or recorded.</obo:IAO_0000115>
<obo:IAO_0000116>In SEPIO, a high-level distinction is made between Statements that are 'Observations' vs 'Assertions'. Observations are statements that report what is observed, and are inherently true in the sense that they reflect an agents particular experience. Assertions are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence'.
This distinction is important because the ultimate truth of observations or findings do not depend on evidence in the same way that the truth of assertions does. Accordingly, any data related to an observation is not treated as evidence, and captured as observations.</obo:IAO_0000116>
<rdfs:comment>An observation reflects only what an agent observed or device recorded. It is therefore considered a matter of fact, rather than a propositional assertion that may or may not be true. This does not mean that the observations or recordings were necessarily accurate or correct - only that they were indeed made by an agent. For example, the observation that "I counted six ducks in the pond" is a matter of fact, even if there are actually seven because I missed one that was hiding in the reeds.</rdfs:comment>
<rdfs:label xml:lang="en">obsolete_observation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000179 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000179">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<rdfs:label xml:lang="en">value set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000180 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000180">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
<owl:Restriction>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000148"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A statement (ie an assertion or finding) that is used as evidence to evaluate the validity of a target assertion or proposition.</obo:IAO_0000115>
<rdfs:comment>Evidence Statements can be 'findings' that summarize data and outcomes from a particular study, or evidence-based 'assertions' that make a broader claim, as inferred from the interpretation and evaluation of previously generated information.</rdfs:comment>
<rdfs:label xml:lang="en">evidence statement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000181 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000181">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000306"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000308"/>
</owl:unionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
</rdf:Description>
</owl:onProperty>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000148"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Research data, or a product derived from research data such as data sets or figures, that are used as evidence to evaluate the validity of a target assertion or proposition.</obo:IAO_0000115>
<obo:IAO_0000116>Evidence data is not classified as a 'data item' because it is intended to cover products derived from data such as figures, tables, and data sets.</obo:IAO_0000116>
<obo:IAO_0000118>evidence datum</obo:IAO_0000118>
<rdfs:comment>Instances of this class can include elemental 'data items' such as experimental measurements or derived statistical calculations or scores (e.g. a 548.5 mg/dl blood glucose level, or a 1.3951e-24 p-value), data sets containing several such values and possibly metadata about them, or tables/figures that render such data for human consumption.
The notion of 'evidence data' is meant to be contrasted with the notion of an 'evidence statement', which is a statement used as evidence. (Statements here are logical sentences with truth value that are typically supported by interpretation of more fundamental data).</rdfs:comment>
<rdfs:label xml:lang="en">evidence data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000185 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000185">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000306"/>
<obo:IAO_0000118>A set of data arranged in rows and columns.</obo:IAO_0000118>
<obo:IAO_0000119>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C48693 ! Data Table</obo:IAO_0000119>
<rdfs:label xml:lang="en">data table</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000186 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000186">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000070"/>
<obo:IAO_0000115>A study with the goal of assessing and documenting phenotypes exhibited by one or more patients.</obo:IAO_0000115>
<rdfs:comment>Source: ClinVar (" 'Phenotyping only' is intended for variants that are submitted to ClinVar to provide individual observations with detailed phenotype data, such as submissions from clinicians or patient registries, without an interpretation from the submitter. The interpretation from the testing laboratory may be provided in a separate field.")
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf</rdfs:comment>
<rdfs:label xml:lang="en">patient phenotyping study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000187 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000187">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000179"/>
<obo:IAO_0000115>A categorical value indicating the degree to which the observation or proposition made in a statement is beleived to be true.</obo:IAO_0000115>
<obo:IAO_0000116>Consider subclasses for 'assertion confidence value' and 'finding confidence value'.</obo:IAO_0000116>
<rdfs:label xml:lang="en">statement confidence level</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000235 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000235">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000179"/>
<obo:IAO_0000115>A data item that is about the frequency with which a phenomenon occurs.</obo:IAO_0000115>
<rdfs:label xml:lang="en">frequency data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000258 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000258">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000070"/>
<rdfs:comment>Source: ClinVar (" 'Provider interpretation' is intended for variants that were interpreted by a clinical provider. For example, the clinician may reclassify the variant using detailed patient phenotype information that was unavailable to the testing laborator")
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf</rdfs:comment>
<rdfs:label xml:lang="en">provider interpretation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">Chi-Squared statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000039 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000039">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000112>
<rdf:Description/>
</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000085 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000085">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB,PRS</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">effect size estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000100 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000100">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SMD</obo:IAO_0000118>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">standardized mean difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000104 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000104">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">z-score</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000123 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000123">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580747/</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">r2</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000135 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000135">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000100"/>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/SSMD</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">strictly standardized mean difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000142 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000142">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000176 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000176">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">t-statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000182 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000182">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label>odds ratio</rdfs:label>
<rdfs:label xml:lang="en">odds ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000184 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000184">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000129"/>
<obo:IAO_0000115>A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.</obo:IAO_0000115>
<rdfs:label>obsolete_ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000193 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000193">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<obo:IAO_0000115>is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.</obo:IAO_0000115>
<rdfs:label>study group population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000201 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000201">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Spearman's rho</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">Spearman's rank correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000212 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000212">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000269"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">tetrachoric correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000240 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000240">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Kendall rank correlation coefficient</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Kendall's tau (τ) coefficient</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">Kendall's correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000245 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000245">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000115>Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus a the probability of this event occurring in the non-exposed group.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>risk ratio</obo:IAO_0000118>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label>relative risk</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000269 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000269">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">polychoric correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000280 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000280">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Pearson product-moment correlation coefficient</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Pearson's r</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">r statistics</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">Pearson's correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000282 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000282">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">F-statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000316 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000316">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">root-mean-square standardized effect is a data item which denotes effect size in the context of analysis of variance and corresponds to the square root of the arithmetic average of p standardized effects (effects normalized to be expressed in standard deviation units).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Ψ</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.statpower.net/Steiger%20Biblio/Steiger04.pdf</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">root-mean-square standardized effect</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000317 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000317">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Eta-squared is a biased estimator of the variance explained by the model in the population (it estimates only the effect size in the sample). Eta-squared describes the ratio of variance explained in the dependent variable by a predictor while controlling for other predictors, making it analogous to the r2. This estimate shares the weakness with r2 that each additional variable will automatically increase the value of η2. In addition, it measures the variance explained of the sample, not the population, meaning that it will always overestimate the effect size, although the bias grows smaller as the sample grows larger.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Effect_size#Eta-squared.2C_.CE.B72</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">eta-squared</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000318 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000318">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">omega-squared is a effect size estimate for variance explained which is less biased than the eta-squared coefficient.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">omega-squared</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000319 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000319">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Hedges's g is an estimator of effect size which is similar to Cohen's d and is a measure based on a standardized difference however the denominator , corresponding to a pooled standard deviation, is computed differently from Cohen's d coefficient, by applying a correction factor (which involves a Gamma function)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">Hedges's g</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000320 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000320">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Glass's delta is an estimator of effect size which is similar to Cohen's d but where the denominator corresponds only to the standard deviation of the control group (or second group). It is considered less biais than the Cohen's d for estimating effect sizes based on means and distances between means.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obofoundry.org/obo/stato.owl"/>
<rdfs:label xml:lang="en">Glass's delta</rdfs:label>
</owl:Class>
<!-- http://purl.org/oban/association -->
<owl:Class rdf:about="http://purl.org/oban/association">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<obo:IAO_0000115>Associations are a form of proposition, framed as a tuple linking two (or more) entities through defined relationships.</obo:IAO_0000115>
<obo:IAO_0000118>annotation</obo:IAO_0000118>
<rdfs:label xml:lang="en">association</rdfs:label>
</owl:Class>
<!-- http://semanticscience.org/resource/SIO_000794 -->
<owl:Class rdf:about="http://semanticscience.org/resource/SIO_000794">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<obo:IAO_0000115>The number of elements of a finite set of objects.</obo:IAO_0000115>
<rdfs:label xml:lang="en">count</rdfs:label>
</owl:Class>
<!-- http://semanticscience.org/resource/SIO_001014 -->
<owl:Class rdf:about="http://semanticscience.org/resource/SIO_001014">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000115>the biological quality of membership in a social group based on a common heritage</obo:IAO_0000115>
<rdfs:label>ethnicity</rdfs:label>
</owl:Class>
<!-- http://semanticscience.org/resource/SIO_001016 -->
<owl:Class rdf:about="http://semanticscience.org/resource/SIO_001016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<obo:IAO_0000115>An ethnic group is a group of people whose members identify with each other through a common heritage, consisting of a common culture, including a shared language or dialect</obo:IAO_0000115>
<rdfs:label>ethnic group</rdfs:label>
</owl:Class>
<!-- http://www.w3.org/ns/prov#Activity -->
<owl:Class rdf:about="http://www.w3.org/ns/prov#Activity">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000160"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#dateTime"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.</obo:IAO_0000115>
<rdfs:label>Activity</rdfs:label>
</owl:Class>
<!-- http://www.w3.org/ns/prov#Agent -->
<owl:Class rdf:about="http://www.w3.org/ns/prov#Agent">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000115>An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.</obo:IAO_0000115>
<obo:IAO_0000116>prov:Agent is considered equivalent to foaf:Agent (http://xmlns.com/foaf/0.1/Agent ) Def = "The Agent class is the class of agents; things that do stuff. A well known sub-class is Person, representing people. Other kinds of agents include Organization and Group."</obo:IAO_0000116>
<rdfs:comment>Agents typically persons, organizations, or software that perform tasks, including making assertions, or generating information used as evidence. In the execution of such tasks, an 'agent role' is realized that inheres in the agent.</rdfs:comment>
<rdfs:label>Agent</rdfs:label>
</owl:Class>
<!-- http://xmlns.com/foaf/0.1/Group -->
<owl:Class rdf:about="http://xmlns.com/foaf/0.1/Group">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000129"/>
<rdfs:comment>The Group class represents a collection of individual agents (and may itself play the role of a Agent, ie. something that can perform actions).
This concept is intentionally quite broad, covering informal and ad-hoc groups, long-lived communities, organizational groups within a workplace, etc. Some such groups may have associated characteristics which could be captured in RDF (perhaps a homepage, name, mailing list etc.).</rdfs:comment>
<rdfs:label>obsolete_Group</rdfs:label>
</owl:Class>
<!-- http://xmlns.com/foaf/0.1/Organization -->
<owl:Class rdf:about="http://xmlns.com/foaf/0.1/Organization">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">Organization</rdfs:label>
</owl:Class>
<!-- http://xmlns.com/foaf/0.1/Person -->
<owl:Class rdf:about="http://xmlns.com/foaf/0.1/Person">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000046"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A human being regarded as an individual.</obo:IAO_0000115>
<rdfs:comment>The Person class represents people. Something is a Person if it is a person. We don't nitpic about whether they're alive, dead, real, or imaginary. The Person class is a sub-class of the Agent class, since all people are considered 'agents' in FOAF.</rdfs:comment>
<rdfs:label xml:lang="en">Person</rdfs:label>
</owl:Class>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// 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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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_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_0000410 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000410">
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf</obo:IAO_0000119>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">universal</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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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/SEPIO_0000236 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000236">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000235"/>
<rdfs:label xml:lang="en">high frequency</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000237 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000237">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000235"/>
<rdfs:label xml:lang="en">low frequency</rdfs:label>
</owl:NamedIndividual>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotations
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<rdf:Description rdf:about="http://example.com/bfo-spec-label">
<obo:IAO_0000119>Person:Alan Ruttenberg</obo:IAO_0000119>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000134">
<obo:IAO_0000600 xml:lang="en">To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])</obo:IAO_0000600>
<obo:IAO_0000600 xml:lang="en">To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])</obo:IAO_0000600>
</rdf:Description>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000134"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/080-003"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000134"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
<owl:annotatedTarget xml:lang="en">To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])</owl:annotatedTarget>
<obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/081-003"/>
</owl:Axiom>
<rdf:Description rdf:about="http://purl.org/dc/terms/source">
<rdfs:label xml:lang="en">source</rdfs:label>
<obo:IAO_0000115>A related resource from which the described resource is derived.</obo:IAO_0000115>
<rdfs:comment>The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.</rdfs:comment>
</rdf:Description>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// General axioms
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AllDifferent"/>
<owl:distinctMembers rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000120"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000121"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000122"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000123"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000124"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000125"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000423"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000428"/>
</owl:distinctMembers>
</rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AllDifferent"/>
<owl:distinctMembers rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000226"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000227"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000228"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000229"/>
</owl:distinctMembers>
</rdf:Description>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->