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Merge pull request #234 from OBOFoundry/fix-233-immmaterial
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Fix BFO:immaterial entity
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@matentzn
matentzn authored May 12, 2023
2 parents 72f24d9 + 0a8eb2e commit 6ae8c0f
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64 changes: 54 additions & 10 deletions cob-base-reasoned.owl
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Original file line number Diff line number Diff line change
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xmlns:sssom="https://w3id.org/sssom/"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-base-reasoned.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-02-19/cob-base-reasoned.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-05-12/cob-base-reasoned.owl"/>
<dc:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</dc:description>
<dc:title xml:lang="en">Core Ontology for Biology and Biomedicine</dc:title>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<owl:versionInfo>2023-02-19</owl:versionInfo>
<owl:versionInfo>2023-05-12</owl:versionInfo>
</owl:Ontology>


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<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>



<!-- http://purl.org/dc/elements/1.1/date -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>



<!-- http://purl.org/dc/elements/1.1/description -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000029">
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/COB_0000057"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000041"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
</owl:Class>
<owl:Axiom>
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<!-- http://purl.obolibrary.org/obo/BFO_0000041 -->
<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000041">
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000041"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
<sssom:mapping_justification rdf:resource="https://w3id.org/semapv/ManualMappingCuration"/>
Expand Down Expand Up @@ -1523,7 +1535,7 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000031">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000041</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000141</obo:COB_based_on>
<rdfs:label xml:lang="en">immaterial entity</rdfs:label>
</owl:Class>

Expand All @@ -1532,7 +1544,7 @@
<!-- http://purl.obolibrary.org/obo/COB_0000032 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000032">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000041"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label xml:lang="en">geographical location</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/COB_0000056 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000056">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000041"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
<rdfs:label>immaterial anatomical entity</rdfs:label>
</owl:Class>
Expand All @@ -1758,7 +1770,7 @@
<!-- http://purl.obolibrary.org/obo/COB_0000057 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000057">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000041"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000029</obo:COB_based_on>
<rdfs:label>site</rdfs:label>
Expand Down Expand Up @@ -2625,6 +2637,38 @@



<!-- http://purl.obolibrary.org/obo/COB_0001300 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001300">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000026"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000028"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000110"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000512"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000112"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A processed material entity which is designed to perform a function.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-8844-9165"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-03-24T16:04:27Z</dc:date>
<rdfs:comment xml:lang="en">In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device.

We say &quot;designed&quot; to emphasize a device&apos;s primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight.

Regarding usage then, we don&apos;t say a naturally formed rock is a hammering device - it wasn&apos;t designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering &quot;tool&quot;, which does not necessarily convey intentional design.

Example of use: A whole device like an engine; a component like a bolt is also a device.</rdfs:comment>
<rdfs:label xml:lang="en">device</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/DRON_0000005 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_0000005">
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55 changes: 49 additions & 6 deletions cob-base.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,12 @@
xmlns:sssom="https://w3id.org/sssom/"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-02-19/cob-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-05-12/cob-base.owl"/>
<dc:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</dc:description>
<dc:title xml:lang="en">Core Ontology for Biology and Biomedicine</dc:title>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<owl:versionInfo>2023-02-19</owl:versionInfo>
<owl:versionInfo>2023-05-12</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -55,6 +55,18 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>



<!-- http://purl.org/dc/elements/1.1/date -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>



<!-- http://purl.org/dc/elements/1.1/description -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
Expand Down Expand Up @@ -816,13 +828,13 @@



<!-- http://purl.obolibrary.org/obo/BFO_0000041 -->
<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000041">
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000041"/>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000031"/>
<sssom:mapping_justification rdf:resource="https://w3id.org/semapv/ManualMappingCuration"/>
Expand Down Expand Up @@ -1456,7 +1468,7 @@
<!-- http://purl.obolibrary.org/obo/COB_0000031 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000031">
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000041</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/BFO_0000141</obo:COB_based_on>
<rdfs:label xml:lang="en">immaterial entity</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -2510,6 +2522,37 @@



<!-- http://purl.obolibrary.org/obo/COB_0001300 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001300">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000026"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000028"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000110"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000512"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000112"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A processed material entity which is designed to perform a function.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:resource="https://orcid.org/0000-0002-8844-9165"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-03-24T16:04:27Z</dc:date>
<rdfs:comment xml:lang="en">In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device.

We say &quot;designed&quot; to emphasize a device&apos;s primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight.

Regarding usage then, we don&apos;t say a naturally formed rock is a hammering device - it wasn&apos;t designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering &quot;tool&quot;, which does not necessarily convey intentional design.

Example of use: A whole device like an engine; a component like a bolt is also a device.</rdfs:comment>
<rdfs:label xml:lang="en">device</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/DRON_0000005 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_0000005"/>
Expand Down
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