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variety of small changes
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@micheldumontier
micheldumontier committed Jul 6, 2021
1 parent bf7c8d1 commit 2f518c8
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Showing 18 changed files with 14,293 additions and 13,992 deletions.
2 changes: 2 additions & 0 deletions .gitignore
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@@ -0,0 +1,2 @@

ontology/catalog-v001.xml
37 changes: 16 additions & 21 deletions ontology/sio.owl
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Expand Up @@ -76,7 +76,7 @@ mailing list: http://groups.google.com/group/sio-ontology
role chains:
&apos;has capability&apos; o &apos;is realized in&apos; -&gt; &apos;is participant in&apos;</schema:comment>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://sio.semanticscience.org</rdfs:seeAlso>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.52</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.53</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -257,8 +257,8 @@ role chains:

<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_000001">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<rdfs:domain rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:range rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:domain rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
<rdfs:range rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
<terms:description xml:lang="en">A is related to B iff there is some relation between A and B.</terms:description>
<schema:comment>&apos;is related to&apos; is the top level relation in SIO</schema:comment>
<sio:subset>core</sio:subset>
Expand All @@ -273,6 +273,7 @@ role chains:
<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_000008">
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000001"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000011"/>
<rdfs:domain rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
<terms:description xml:lang="en">has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.</terms:description>
<sio:subset>core</sio:subset>
<rdfs:label xml:lang="en">has attribute</rdfs:label>
Expand Down Expand Up @@ -359,6 +360,7 @@ role chains:
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000008"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000095"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#IrreflexiveProperty"/>
<rdfs:domain rdf:resource="http://semanticscience.org/resource/SIO_000616"/>
<terms:description xml:lang="en">has member is a mereological relation between a collection and an item.</terms:description>
<sio:subset>core</sio:subset>
<rdfs:label xml:lang="en">has member</rdfs:label>
Expand All @@ -382,7 +384,7 @@ role chains:
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000322"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000145"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<terms:description xml:lang="en">A is located in B iff the spatial region occupied by A is part of the spatial region occupied by B. [T][R]</terms:description>
<terms:description xml:lang="en">A is located in B iff the spatialtemporial region occupied by A is part of the spatialtemporal region occupied by B. [T][R]</terms:description>
<sio:equivalentTo>OBO_REL:located_in</sio:equivalentTo>
<sio:subset>core</sio:subset>
<rdfs:label xml:lang="en">is located in</rdfs:label>
Expand Down Expand Up @@ -532,7 +534,7 @@ role chains:
<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_000145">
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000322"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<terms:description xml:lang="en">A is location of B iff the spatial region occupied by A has the spatial region occupied by B as a part. [T][R]</terms:description>
<terms:description xml:lang="en">A is location of B iff the spatialtemporal region occupied by A has the spatialtemporal region occupied by B as a part. [T][R]</terms:description>
<sio:subset>nlp+</sio:subset>
<rdfs:label xml:lang="en">is location of</rdfs:label>
</owl:ObjectProperty>
Expand Down Expand Up @@ -750,6 +752,7 @@ role chains:
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000008"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000222"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:domain rdf:resource="http://semanticscience.org/resource/SIO_000075"/>
<rdfs:range rdf:resource="http://semanticscience.org/resource/SIO_000074"/>
<terms:description xml:lang="en">has unit is a relation between a quantity and the unit it is a multiple of.</terms:description>
<sio:subset>core</sio:subset>
Expand Down Expand Up @@ -1490,6 +1493,8 @@ role chains:
<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_000362">
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000008"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000363"/>
<rdfs:domain rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
<rdfs:range rdf:resource="http://semanticscience.org/resource/SIO_000136"/>
<terms:description xml:lang="en">satisfies is a relation between an entity and the specification or objective that it conforms to.</terms:description>
<rdfs:label xml:lang="en">satisfies</rdfs:label>
</owl:ObjectProperty>
Expand All @@ -1510,6 +1515,8 @@ role chains:
<owl:ObjectProperty rdf:about="http://semanticscience.org/resource/SIO_000364">
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000253"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000365"/>
<rdfs:domain rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
<rdfs:range rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
<terms:alternative xml:lang="en">is created by</terms:alternative>
<terms:alternative xml:lang="en">was created by</terms:alternative>
<terms:description xml:lang="en">has creator is a relation between an entity and that which created it.</terms:description>
Expand Down Expand Up @@ -8554,17 +8561,6 @@ of endpoints (a start point and an endpoint).</terms:description>
<!-- http://semanticscience.org/resource/SIO_000612 -->

<owl:Class rdf:about="http://semanticscience.org/resource/SIO_000612">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://semanticscience.org/resource/SIO_000015"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://semanticscience.org/resource/SIO_000210"/>
<owl:allValuesFrom rdf:resource="http://semanticscience.org/resource/SIO_000000"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/SIO_000015"/>
<rdfs:subClassOf>
<owl:Restriction>
Expand Down Expand Up @@ -10111,7 +10107,6 @@ of endpoints (a start point and an endpoint).</terms:description>
<!-- http://semanticscience.org/resource/SIO_000779 -->

<owl:Class rdf:about="http://semanticscience.org/resource/SIO_000779">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/SIO_011125"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
Expand Down Expand Up @@ -17889,7 +17884,7 @@ The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pl
<owl:someValuesFrom rdf:resource="http://semanticscience.org/resource/SIO_010004"/>
</owl:Restriction>
</rdfs:subClassOf>
<terms:description xml:lang="en">A submolecular entity is a part of a molecule or a particle smaller than a molecule.</terms:description>
<terms:description xml:lang="en">A submolecular entity is a chemical entity that is a part of a molecule.</terms:description>
<rdfs:label xml:lang="en">submolecular entity</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -19282,7 +19277,7 @@ The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pl
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<terms:description xml:lang="en">A chemical complex is a chemical substance composed of a weakly connected molecules and ions in a known stoichiometry.</terms:description>
<terms:description xml:lang="en">A chemical complex is a chemical substance composed of weakly connected molecules and ions in a known stoichiometry.</terms:description>
<rdfs:label xml:lang="en">chemical complex</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -22516,7 +22511,7 @@ and having their side chains perpendicular to the planar axis.</terms:descriptio
<owl:someValuesFrom rdf:resource="http://semanticscience.org/resource/SIO_010044"/>
</owl:Restriction>
</rdfs:subClassOf>
<terms:description xml:lang="en">A molecule is single chemical entity composed of fully covalently bonded atoms.</terms:description>
<terms:description xml:lang="en">A molecule is a single chemical entity composed of fully covalently bonded atoms.</terms:description>
<rdfs:label xml:lang="en">molecule</rdfs:label>
<skos:exactMatch>CHEBI:23367</skos:exactMatch>
</owl:Class>
Expand All @@ -22536,7 +22531,7 @@ and having their side chains perpendicular to the planar axis.</terms:descriptio
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/SIO_010004"/>
<terms:alternative xml:lang="en">mixture</terms:alternative>
<terms:description xml:lang="en">A chemical substance is a chemical entity composed of two or more weakly interacting chemical entities.</terms:description>
<terms:description xml:lang="en">A chemical substance is a chemical entity composed of two or more weakly (non-covalently) interacting chemical entities.</terms:description>
<rdfs:label xml:lang="en">chemical substance</rdfs:label>
<skos:exactMatch>CHEMINF:440533</skos:exactMatch>
</owl:Class>
Expand Down

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