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ro_subset.owl
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ro_subset.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/ro/ro-base.owl#"
xml:base="http://purl.obolibrary.org/obo/ro/ro-base.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="https://raw.githubusercontent.com/neel-lab/GlycoEnzOnto/main/ro_subset.owl">
<owl:versionIRI rdf:resource="https://raw.githubusercontent.com/neel-lab/GlycoEnzOnto/main/ro_subset.owl"/>
<dc:description xml:lang="en">The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.</dc:description>
<dc:title xml:lang="en">OBO Relations Ontology</dc:title>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 7]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl>) VersionIRI(<null>))) [Axioms: 49 Logical Axioms: 12]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/chemical.owl>) VersionIRI(<null>))) [Axioms: 9 Logical Axioms: 3]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>) VersionIRI(<null>))) [Axioms: 310 Logical Axioms: 68]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>) VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/generated-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 9]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>) VersionIRI(<null>))) [Axioms: 731 Logical Axioms: 148]</rdfs:comment>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>) VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45]</rdfs:comment>
<foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"> https://github.com/oborel/obo-relations/</foaf:homepage>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000424 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000424"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000589 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000589"/>
<!-- http://purl.obolibrary.org/obo/RO_0001900 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900">
<obo:IAO_0000115>An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.</obo:IAO_0000115>
<rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002423 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002423">
<rdfs:label xml:lang="en">logical macro assertion on an annotation property</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002575 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002575">
<obo:IAO_0000115>relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y</obo:IAO_0000115>
<obo:IAO_0000116>The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"</obo:IAO_0000116>
<obo:RO_0002423>If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'</obo:RO_0002423>
<terms:creator>Chris Mungall</terms:creator>
<rdfs:label>is direct form of</rdfs:label>
<rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/RO_0040042 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0040042">
<obo:IAO_0000112>part-of is homeomorphic for independent continuants.</obo:IAO_0000112>
<obo:IAO_0000115>R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.</obo:IAO_0000115>
<oboInOwl:created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-10-21T19:46:34Z</oboInOwl:creation_date>
<rdfs:comment>R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.</rdfs:comment>
<rdfs:label>is homeomorphic for</rdfs:label>
<rdfs:seeAlso rdf:resource="https://github.com/oborel/obo-relations/issues/164"/>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
<!-- http://purl.org/dc/elements/1.1/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
<!-- http://purl.org/dc/elements/1.1/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
<!-- http://purl.org/dc/terms/creator -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://purl.org/dc/terms/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/source"/>
<!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
<!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_related_synonym</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_subset</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.w3.org/2000/01/rdf-schema#comment -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
<!-- http://www.w3.org/2000/01/rdf-schema#isDefinedBy -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#isDefinedBy">
<obo:IAO_0000589>is defined by</obo:IAO_0000589>
</owl:AnnotationProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://www.w3.org/2000/01/rdf-schema#isDefinedBy"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000589"/>
<owl:annotatedTarget>is defined by</owl:annotatedTarget>
<rdfs:comment>This is an experimental annotation</rdfs:comment>
</owl:Axiom>
<!-- http://www.w3.org/2000/01/rdf-schema#label -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<!-- http://www.w3.org/2000/01/rdf-schema#seeAlso -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#seeAlso"/>
<!-- http://www.w3.org/2004/02/skos/core#closeMatch -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#closeMatch"/>
<!-- 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">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<obo:IAO_0000111 xml:lang="en">is part of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my brain is part of my body (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this day is part of this year (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a part and its whole</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:RO_0040042 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
<rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"/>
<rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:PartOf"/>
<rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<obo:IAO_0000111 xml:lang="en">has part</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my body has part my brain (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this year has part this day (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a whole and its part</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000062 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000062">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002086"/>
<obo:IAO_0000111 xml:lang="en">preceded by</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is preceded by</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">preceded_by</obo:IAO_0000118>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</dc:source>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">preceded by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000063 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000063">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000111 xml:lang="en">precedes</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000066 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000066">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000111 xml:lang="en">occurs in</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">occurs_in</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">unfolds in</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">unfolds_in</obo:IAO_0000118>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:comment>Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">occurs in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000111 xml:lang="en">participates in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood clot participates in this blood coagulation</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this input material (or this output material) participates in this process</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigator participates in this investigation</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">participates_in</obo:IAO_0000118>
<rdfs:label xml:lang="en">participates in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<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>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</dc:source>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001025 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001025">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000111 xml:lang="en">located in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my brain is located in my head</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this rat is located in this cage</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between two independent continuants, the target and the location, in which the target is entirely within the location</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">located_in</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:located_in</dc:source>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<rdfs:label xml:lang="en">located in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002012 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002012">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
<obo:IAO_0000115>A part of relation that applies only between occurrents.</obo:IAO_0000115>
<rdfs:label>occurrent part of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002084 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002084">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment>Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.</rdfs:comment>
<rdfs:label xml:lang="en">during which ends</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002085 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002085">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002084"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002088"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>di</obo:IAO_0000118>
<rdfs:comment>Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.</rdfs:comment>
<rdfs:label xml:lang="en">encompasses</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002086 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002086">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment xml:lang="en">X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)</rdfs:comment>
<rdfs:label xml:lang="en">ends after</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002088 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002088">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment>Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.</rdfs:comment>
<rdfs:label xml:lang="en">during which starts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002090 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002090">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>ends_at_start_of</obo:IAO_0000118>
<obo:IAO_0000118>meets</obo:IAO_0000118>
<obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment xml:lang="en">X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)</rdfs:comment>
<rdfs:label xml:lang="en">immediately precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002091 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002091">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>io</obo:IAO_0000118>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment xml:lang="en">X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))</rdfs:comment>
<rdfs:label xml:lang="en">starts during</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002092 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002092">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002091"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002093"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>d</obo:IAO_0000118>
<obo:IAO_0000118>during</obo:IAO_0000118>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment xml:lang="en">X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))</rdfs:comment>
<rdfs:label xml:lang="en">happens during</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002093 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002093">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>o</obo:IAO_0000118>
<obo:IAO_0000118>overlaps</obo:IAO_0000118>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment xml:lang="en">X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). </rdfs:comment>
<rdfs:label xml:lang="en">ends during</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002131 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002131">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>x overlaps y if and only if there exists some z such that x has part z and z part of y</obo:IAO_0000115>
<obo:IAO_0000424>http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)</obo:IAO_0000424>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">overlaps</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002215 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002215">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002216"/>
<obo:IAO_0000112>mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)</obo:IAO_0000112>
<obo:IAO_0000112>osteoclast SubClassOf 'capable of' some 'bone resorption'</obo:IAO_0000112>
<obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. </obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has function realized in</obo:IAO_0000118>
<obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/20123131"/>
<obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21208450"/>
<obo:IAO_0000232>For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".</obo:IAO_0000232>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">capable of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002216 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002216">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
<obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has function in</obo:IAO_0000118>
<rdfs:label xml:lang="en">capable of part of</rdfs:label>
<rdfs:seeAlso rdf:resource="http://purl.obolibrary.org/obo/ro/docs/reflexivity/"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002222 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002222">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="https://en.wikipedia.org/wiki/Allen%27s_interval_algebra"/>
<obo:IAO_0000232>Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.</obo:IAO_0000232>
<terms:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1</terms:source>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:comment>A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.</rdfs:comment>
<rdfs:label xml:lang="en">temporally related to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002223 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002223">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of starts with</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119>Allen</obo:IAO_0000119>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">starts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002224 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002224">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000112>Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>started by</obo:IAO_0000118>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">starts with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002264 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002264">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
<obo:IAO_0000112>A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.</obo:IAO_0000112>
<obo:IAO_0000115>c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.</obo:IAO_0000115>
<oboInOwl:hasRelatedSynonym>affects</oboInOwl:hasRelatedSynonym>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<rdfs:label>acts upstream of or within</rdfs:label>
<rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002323 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002323">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000115>A mereological relationship or a topological relationship</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000232>Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships</obo:IAO_0000232>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">mereotopologically related to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002327 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002327">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002215"/>
<obo:IAO_0000112>a particular instances of akt-2 enables some instance of protein kinase activity</obo:IAO_0000112>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>catalyzes</obo:IAO_0000118>
<obo:IAO_0000118>executes</obo:IAO_0000118>
<obo:IAO_0000118>has</obo:IAO_0000118>
<obo:IAO_0000118>is catalyzing</obo:IAO_0000118>
<obo:IAO_0000118>is executing</obo:IAO_0000118>
<obo:IAO_0000232>This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.</obo:IAO_0000232>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<rdfs:label xml:lang="en">enables</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002328 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002328">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000115>A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000232>This is a grouping relation that collects relations used for the purpose of connecting structure and function</obo:IAO_0000232>
<rdfs:label xml:lang="en">functionally related to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002331 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
<obo:IAO_0000115>c involved_in p if and only if c enables some process p', and p' is part of p</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>actively involved in</obo:IAO_0000118>
<obo:IAO_0000118>enables part of</obo:IAO_0000118>
<rdfs:label xml:lang="en">involved in</rdfs:label>
<rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Involved_in"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002333 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002333">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
<obo:IAO_0000115>inverse of enables</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">enabled by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002410 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002410">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>This relation groups causal relations between material entities and causal relations between processes</obo:IAO_0000115>
<obo:IAO_0000116>This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000232>Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.</obo:IAO_0000232>
<rdfs:label xml:lang="en">causally related to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002411 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002411">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">causally upstream of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002412 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002412">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002090"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<rdfs:label xml:lang="en">immediately causally upstream of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002413 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002413">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002412"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002414"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c</obo:IAO_0000115>
<obo:IAO_0000116>This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000589>directly provides input for (process to process)</obo:IAO_0000589>
<rdfs:label xml:lang="en">directly provides input for</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002414 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002414">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>transitive form of directly_provides_input_for</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000232>This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')</obo:IAO_0000232>
<obo:IAO_0000589>transitively provides input for (process to process)</obo:IAO_0000589>
<rdfs:label xml:lang="en">transitively provides input for</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002418 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002418">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002501"/>
<obo:IAO_0000115>p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.</obo:IAO_0000115>
<obo:IAO_0000116>We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>influences (processual)</obo:IAO_0000118>
<oboInOwl:hasRelatedSynonym>affects</oboInOwl:hasRelatedSynonym>
<rdfs:label>causally upstream of or within</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002431 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002431">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
<obo:IAO_0000115>c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p</obo:IAO_0000115>
<obo:IAO_0000116>OWL does not allow defining object properties via a Union</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>involved in or reguates</obo:IAO_0000118>
<rdfs:label>involved in or involved in regulation of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002434 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002434">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>A relationship that holds between two entities in which the processes executed by the two entities are causally connected.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">Considering relabeling as 'pairwise interacts with'</obo:IAO_0000116>
<obo:IAO_0000116>This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000232>Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.</obo:IAO_0000232>
<oboInOwl:hasExactSynonym>in pairwise interaction with</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label>interacts with</rdfs:label>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/ro/docs/interaction-relations/</rdfs:seeAlso>
<skos:closeMatch rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/MI_0914</skos:closeMatch>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002435 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002435">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002434"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002436 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002436">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002434"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002437 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002437">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002434"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002500 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002500">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002595"/>
<obo:IAO_0000115>A relationship between a material entity and a process where the material entity has some causal role that influences the process</obo:IAO_0000115>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<rdfs:label>causal agent in process</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002501 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002501">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002410"/>
<obo:IAO_0000115>p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000232>Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.</obo:IAO_0000232>
<rdfs:label>causal relation between processes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002595 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002595">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002410"/>
<obo:IAO_0000115>A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.</obo:IAO_0000115>
<obo:IAO_0000116>Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<rdfs:label>causal relation between material entity and a process</rdfs:label>
</owl:ObjectProperty>
<!-- http://www.w3.org/2002/07/owl#topObjectProperty -->
<owl:ObjectProperty rdf:about="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
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-->
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->