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added inverse of model-of
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@cmungall
cmungall committed Aug 9, 2015
1 parent d71a1a8 commit 6ff37d4
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Showing 19 changed files with 5,425 additions and 1,013 deletions.
7 changes: 6 additions & 1 deletion bfo-classes-minimal.owl
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Expand Up @@ -88,6 +88,11 @@
<obo:IAO_0000115 xml:lang="en">An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.</obo:IAO_0000115>
</owl:Class>

<owl:Class rdf:about="&obo;BFO_0000016">
<rdfs:label xml:lang="en">disposition</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;BFO_0000017"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
Expand Down Expand Up @@ -143,7 +148,7 @@

<owl:Class rdf:about="&obo;BFO_0000034">
<rdfs:label xml:lang="en">function</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;BFO_0000017"/>
<rdfs:subClassOf rdf:resource="&obo;BFO_0000016"/>
</owl:Class>


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19 changes: 15 additions & 4 deletions ro.obo
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148 changes: 79 additions & 69 deletions ro.owl
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146 changes: 78 additions & 68 deletions src/ontology/ro-edit.owl
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5,543 changes: 4,933 additions & 610 deletions src/ontology/ro-el.owl
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19 changes: 15 additions & 4 deletions src/ontology/ro.obo
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148 changes: 79 additions & 69 deletions src/ontology/ro.owl
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32 changes: 16 additions & 16 deletions src/ontology/subsets/ro-causal.owl
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Expand Up @@ -349,7 +349,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:domain>
<rdfs:range>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000002"/>
Expand All @@ -359,8 +359,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range>
</rdfs:range>
<rdfs:domain>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000002"/>
Expand All @@ -370,7 +370,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:range>
</rdfs:domain>
</owl:ObjectProperty>


Expand Down Expand Up @@ -941,22 +941,22 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002202"/>
<obo:RO_0002575 rdf:resource="http://purl.obolibrary.org/obo/RO_0002202"/>
<rdfs:domain>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CARO_0010000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000000"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range>
</rdfs:range>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CARO_0010000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000000"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
</rdfs:domain>
</owl:ObjectProperty>


Expand Down Expand Up @@ -2160,9 +2160,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedTarget>Deschutes River tributary_of Columbia River</owl:annotatedTarget>
<dc:source>GAZ</dc:source>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
<owl:annotatedTarget>drains to</owl:annotatedTarget>
<dc:source rdf:resource="http://dbpedia.org/ontology/drainsTo"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002376"/>
</owl:Axiom>
<owl:Axiom>
Expand All @@ -2172,9 +2172,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002376"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget>drains to</owl:annotatedTarget>
<dc:source rdf:resource="http://dbpedia.org/ontology/drainsTo"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedTarget>Deschutes River tributary_of Columbia River</owl:annotatedTarget>
<dc:source>GAZ</dc:source>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002376"/>
</owl:Axiom>

Expand All @@ -2197,8 +2197,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedTarget>Deschutes River distributary_of Little Lava Lake</owl:annotatedTarget>
<dc:source>GAZ</dc:source>
<owl:annotatedTarget>Deschutes River distributary_of Little Lava Lake</owl:annotatedTarget>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002377"/>
</owl:Axiom>
Expand Down Expand Up @@ -4238,8 +4238,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002597"/>
</owl:ObjectProperty>
<owl:Axiom>
<rdfs:comment>Usage of the term &apos;treats&apos; applies when we believe there to be a an inhibitory relationship</rdfs:comment>
<owl:annotatedTarget>treats</owl:annotatedTarget>
<rdfs:comment>Usage of the term &apos;treats&apos; applies when we believe there to be a an inhibitory relationship</rdfs:comment>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002599"/>
</owl:Axiom>
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24 changes: 12 additions & 12 deletions src/ontology/subsets/ro-developmental.owl
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Expand Up @@ -613,9 +613,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
<rdfs:label xml:lang="en">has synaptic terminal in</rdfs:label>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002130</oboInOwl:hasDbXref>
<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_synaptic_terminal_in</oboInOwl:shorthand>
<obo:IAO_0000115>A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.</obo:IAO_0000115>
<obo:IAO_0000118>has synapse in</obo:IAO_0000118>
<obo:IAO_0000424>&lt;http://purl.obolibrary.org/obo/RO_0002131&gt; some (&lt;http://purl.obolibrary.org/obo/GO_0045202&gt; that &lt;http://purl.obolibrary.org/obo/BFO_0000050&gt; some Y?)</obo:IAO_0000424>
<obo:IAO_0000115>A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
Expand Down Expand Up @@ -788,18 +788,18 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000</obo:IAO_0000115>
<obo:IAO_0000115>a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b</obo:IAO_0000115>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
<obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/22293552"/>
<rdfs:domain>
<rdfs:range>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/RO_0002577"/>
</owl:Restriction>
</rdfs:domain>
<rdfs:range>
</rdfs:range>
<rdfs:domain>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/RO_0002577"/>
</owl:Restriction>
</rdfs:range>
</rdfs:domain>
</owl:ObjectProperty>


Expand Down Expand Up @@ -2159,12 +2159,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002375"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedTarget>Deschutes River tributary_of Columbia River</owl:annotatedTarget>
<dc:source>GAZ</dc:source>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002376"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget>drains to</owl:annotatedTarget>
<dc:source rdf:resource="http://dbpedia.org/ontology/drainsTo"/>
Expand All @@ -2177,6 +2171,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002376"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget>Deschutes River tributary_of Columbia River</owl:annotatedTarget>
<dc:source>GAZ</dc:source>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000112"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002376"/>
</owl:Axiom>



Expand Down Expand Up @@ -4238,8 +4238,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002597"/>
</owl:ObjectProperty>
<owl:Axiom>
<rdfs:comment>Usage of the term &apos;treats&apos; applies when we believe there to be a an inhibitory relationship</rdfs:comment>
<owl:annotatedTarget>treats</owl:annotatedTarget>
<rdfs:comment>Usage of the term &apos;treats&apos; applies when we believe there to be a an inhibitory relationship</rdfs:comment>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002599"/>
</owl:Axiom>
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6 changes: 6 additions & 0 deletions src/ontology/subsets/ro-eco.obo
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Expand Up @@ -2936,6 +2936,12 @@ def: "A relationship that holds between two entities, where the entities exhibit
property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string
is_a: RO:0002609 ! related via dependence to

[Typedef]
id: RO:0002615
name: has model
def: "Inverse of is-model-of" []
inverse_of: RO:0003301 ! is model of

[Typedef]
id: RO:0003000
name: produces
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