diff --git a/cob-base-reasoned.owl b/cob-base-reasoned.owl
index e5cf056..6fdd3ae 100644
--- a/cob-base-reasoned.owl
+++ b/cob-base-reasoned.owl
@@ -12,12 +12,12 @@
xmlns:sssom="http://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/2022-05-02/cob-base-reasoned.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -1013,7 +1013,6 @@
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/COB_0000118"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
@@ -1669,12 +1668,10 @@
<!-- http://purl.obolibrary.org/obo/COB_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
- <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001010</obo:COB_based_on>
- <obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_1</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
<obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
<rdfs:comment>"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.</rdfs:comment>
@@ -1689,14 +1686,6 @@
<sssom:object_label>organism or virus or viroid</sssom:object_label>
<sssom:subject_label>organism</sssom:subject_label>
</owl:Axiom>
- <owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
- <sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
- </owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
@@ -2788,7 +2777,6 @@
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0010004</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_131567</obo:COB_based_on>
@@ -2958,6 +2946,17 @@
+ <!-- http://purl.obolibrary.org/obo/COB_0001000 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000034"/>
+ <obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">exposure of organism</rdfs:label>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/DRON_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_0000005">
@@ -3227,19 +3226,20 @@
- <!-- http://purl.obolibrary.org/obo/NCBITaxon_1 -->
+ <!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1">
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>Viruses</sssom:subject_label>
</owl:Axiom>
@@ -3249,7 +3249,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
@@ -3260,6 +3259,14 @@
<sssom:object_label>cellular organisms</sssom:object_label>
<sssom:subject_label>cellular organism</sssom:subject_label>
</owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ <sssom:match_type>HumanCurated</sssom:match_type>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>cellular organisms</sssom:subject_label>
+ </owl:Axiom>
diff --git a/cob-base.owl b/cob-base.owl
index 48c6988..fda6dbb 100644
--- a/cob-base.owl
+++ b/cob-base.owl
@@ -12,12 +12,12 @@
xmlns:sssom="http://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/2022-05-02/cob-base.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -1605,11 +1605,9 @@
<!-- http://purl.obolibrary.org/obo/COB_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
- <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001010</obo:COB_based_on>
- <obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_1</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
<obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
<rdfs:comment>"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.</rdfs:comment>
@@ -1624,14 +1622,6 @@
<sssom:object_label>organism or virus or viroid</sssom:object_label>
<sssom:subject_label>organism</sssom:subject_label>
</owl:Axiom>
- <owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
- <sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
- </owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
@@ -2842,6 +2832,16 @@
+ <!-- http://purl.obolibrary.org/obo/COB_0001000 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000034"/>
+ <obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">exposure of organism</rdfs:label>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/DRON_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_0000005"/>
@@ -3068,23 +3068,27 @@
- <!-- http://purl.obolibrary.org/obo/NCBITaxon_1 -->
+ <!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ </owl:Class>
<owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>Viruses</sssom:subject_label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_131567 -->
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ </owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000118"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
@@ -3093,6 +3097,14 @@
<sssom:object_label>cellular organisms</sssom:object_label>
<sssom:subject_label>cellular organism</sssom:subject_label>
</owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ <sssom:match_type>HumanCurated</sssom:match_type>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>cellular organisms</sssom:subject_label>
+ </owl:Axiom>
diff --git a/cob-examples-reasoned.owl b/cob-examples-reasoned.owl
index b4b77be..2814bd2 100644
--- a/cob-examples-reasoned.owl
+++ b/cob-examples-reasoned.owl
@@ -12,12 +12,12 @@
xmlns:sssom="http://w3id.org/sssom/"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-examples-reasoned.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob-examples-reasoned.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/cob-examples-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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -1019,7 +1019,6 @@
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/COB_0000118"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
@@ -1978,12 +1977,10 @@
<!-- http://purl.obolibrary.org/obo/COB_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
- <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001010</obo:COB_based_on>
- <obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_1</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
<obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
<rdfs:comment>"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.</rdfs:comment>
@@ -1998,14 +1995,6 @@
<sssom:object_label>organism or virus or viroid</sssom:object_label>
<sssom:subject_label>organism</sssom:subject_label>
</owl:Axiom>
- <owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
- <sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
- </owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
@@ -3114,7 +3103,6 @@
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0010004</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_131567</obo:COB_based_on>
@@ -3284,6 +3272,17 @@
+ <!-- http://purl.obolibrary.org/obo/COB_0001000 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000034"/>
+ <obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">exposure of organism</rdfs:label>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/DRON_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_0000005">
@@ -3611,19 +3610,20 @@
- <!-- http://purl.obolibrary.org/obo/NCBITaxon_1 -->
+ <!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1">
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>Viruses</sssom:subject_label>
</owl:Axiom>
@@ -3633,7 +3633,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
@@ -3644,6 +3643,14 @@
<sssom:object_label>cellular organisms</sssom:object_label>
<sssom:subject_label>cellular organism</sssom:subject_label>
</owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ <sssom:match_type>HumanCurated</sssom:match_type>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>cellular organisms</sssom:subject_label>
+ </owl:Axiom>
diff --git a/cob-full.owl b/cob-full.owl
index 2c3f113..52559fb 100644
--- a/cob-full.owl
+++ b/cob-full.owl
@@ -11,11 +11,11 @@
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-full.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob-full.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/cob-full.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>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -614,7 +614,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001010</obo:COB_based_on>
- <obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_1</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
<obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
<rdfs:comment>"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.</rdfs:comment>
@@ -1418,6 +1417,16 @@
</owl:annotatedTarget>
<rdfs:comment>We should name the inverse in COB and avoid the confusing inverse(..) construct</rdfs:comment>
</owl:Axiom>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/COB_0001000 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000034"/>
+ <obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">exposure of organism</rdfs:label>
+ </owl:Class>
</rdf:RDF>
diff --git a/cob-native.owl b/cob-native.owl
index 82f865f..ed9ed8b 100644
--- a/cob-native.owl
+++ b/cob-native.owl
@@ -11,11 +11,11 @@
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-native.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob-native.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/cob-native.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>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -1346,6 +1346,16 @@
</owl:annotatedTarget>
<rdfs:comment>We should name the inverse in COB and avoid the confusing inverse(..) construct</rdfs:comment>
</owl:Axiom>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/COB_0001000 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000034"/>
+ <obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">exposure of organism</rdfs:label>
+ </owl:Class>
</rdf:RDF>
diff --git a/cob.owl b/cob.owl
index c8d2cde..8017773 100644
--- a/cob.owl
+++ b/cob.owl
@@ -11,12 +11,12 @@
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/cob.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>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<rdfs:comment xml:lang="en">This version of COB includes native OBO URIs, only using COB IRIs where equivalent natives could not be found. To see the edition that includes native IRIs, consult cob-edit.owl.</rdfs:comment>
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -460,22 +460,10 @@
- <!-- http://purl.obolibrary.org/obo/CARO_0001010 -->
-
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0001010">
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
- <obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
- <rdfs:comment>"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.</rdfs:comment>
- <rdfs:comment>Includes virus - we will later have a class for cellular organisms.</rdfs:comment>
- <rdfs:label xml:lang="en">organism</rdfs:label>
- </owl:Class>
-
-
-
<!-- http://purl.obolibrary.org/obo/CARO_0010004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0010004">
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:label xml:lang="en">cellular organism</rdfs:label>
</owl:Class>
@@ -843,6 +831,16 @@
+ <!-- http://purl.obolibrary.org/obo/COB_0001000 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">exposure of organism</rdfs:label>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/DRON_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_0000005">
@@ -927,18 +925,18 @@
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000066"/>
- <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
+ <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
- <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
+ <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
- <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
+ <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
@@ -1207,6 +1205,18 @@
+ <!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100026">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+ <obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
+ <rdfs:comment>"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.</rdfs:comment>
+ <rdfs:comment>Includes virus - we will later have a class for cellular organisms.</rdfs:comment>
+ <rdfs:label xml:lang="en">organism</rdfs:label>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/OBI_0200000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200000">
diff --git a/cob.tsv b/cob.tsv
index 7753b81..5f0532c 100644
--- a/cob.tsv
+++ b/cob.tsv
@@ -8,8 +8,7 @@ BFO:0000034 function BFO:0000016 disposition
BFO:0000040 material entity
BFO:0000041 immaterial entity
CARO:0001008 gross anatomical part A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. BFO:0000040 material entity
-CARO:0001010 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. BFO:0000040 material entity
-CARO:0010004 cellular organism CARO:0001010 organism
+CARO:0010004 cellular organism OBI:0100026 organism
CHEBI:10545 electron CHEBI:36342|COB:0000013 molecular entity|subatomic particle COB:0000801 value 0 has number of atomic nuclei value 0
CHEBI:24636 proton CHEBI:36342 subatomic particle
CHEBI:24867 monoatomic ion COB:0000011 atom
@@ -37,13 +36,14 @@ COB:0000119 evaluant role BFO:0000023 role
COB:0000120 information representation PATO:0000001 characteristic
COB:0000121 measurement datum IAO:0000027 data item
COB:0000122 physical information carrier BFO:0000040 material entity
+COB:0001000 exposure of organism A process during which an organism comes into contact with another entity. BFO:0000015 process
DRON:0000005 drug product A processed material entity created to be administered to an individual with the intent to improve health. OBI:0000047 processed material entity
ENVO:01000813 geophysical entity BFO:0000040 material entity
ENVO:01001110 ecosystem BFO:0000040 material entity
ENVO:02500000 environmental process BFO:0000015 process
GO:0003674 gene product or complex activity BFO:0000015 process RO:0002333 some (COB:0000073 or GO:0032991) enabled by some (gene product or protein-containing macromolecular complex)
GO:0005634 cell nucleus COB:0000020 subcellular structure
-GO:0008150 biological process A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. BFO:0000015 process (BFO:0000066 some CARO:0001010) or (RO:0000057 some CARO:0001010) or (RO:0000057 some (BFO:0000050 some CARO:0001010))|BFO:0000051 some GO:0003674 (occurs in some organism) or (has participant some organism) or (has participant some (part of some organism))|has part some gene product or complex activity
+GO:0008150 biological process A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. BFO:0000015 process (BFO:0000066 some OBI:0100026) or (RO:0000057 some OBI:0100026) or (RO:0000057 some (BFO:0000050 some OBI:0100026))|BFO:0000051 some GO:0003674 (occurs in some organism) or (has participant some organism) or (has participant some (part of some organism))|has part some gene product or complex activity
GO:0032991 protein-containing macromolecular complex COB:0000080 complex of molecular entities BFO:0000051 some COB:0000073 has part some gene product
IAO:0000005 objective specification IAO:0000033 directive information entity
IAO:0000027 data item IAO:0000030 information
@@ -60,6 +60,7 @@ OBI:0000094 material processing OBI:0000011 completely executed planned process
OBI:0000245 organization BFO:0000040 material entity
OBI:0000260 plan BFO:0000017|COB:0000120 information representation|realizable inverse (COB:0000087) only COB:0000082|COB:0000078 some IAO:0000104 inverse (realizes) only planned process|concretizes some plan specification
OBI:0001909 conclusion based on data IAO:0000030 information
+OBI:0100026 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. BFO:0000040 material entity
OBI:0200000 data transformation OBI:0000011 completely executed planned process
OGMS:0000014 phenotypic finding IAO:0000030 information
OGMS:0000063 disease course BFO:0000015 process
diff --git a/src/ontology/components/cob-annotations.owl b/src/ontology/components/cob-annotations.owl
index 7a4d499..6014727 100644
--- a/src/ontology/components/cob-annotations.owl
+++ b/src/ontology/components/cob-annotations.owl
@@ -8,7 +8,7 @@
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/components/cob-annotations.owl">
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -81,9 +81,8 @@
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001008</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
- <obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
<obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001010</obo:COB_based_on>
- <obo:COB_based_on>http://purl.obolibrary.org/obo/NCBITaxon_1</obo:COB_based_on>
+ <obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000025">
<obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0000245</obo:COB_based_on>
diff --git a/src/ontology/components/cob-to-external.owl b/src/ontology/components/cob-to-external.owl
index f399606..c45d5ae 100644
--- a/src/ontology/components/cob-to-external.owl
+++ b/src/ontology/components/cob-to-external.owl
@@ -10,10 +10,10 @@
xmlns:sssom="http://w3id.org/sssom/"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/components/cob-to-external.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-05-02/components/cob-to-external.owl"/>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/components/cob-to-external.owl"/>
<terms:license rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://creativecommons.org/publicdomain/zero/1.0/</terms:license>
<sssom:mapping_set_id rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/cob/components/cob-to-external.tsv</sssom:mapping_set_id>
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-05-02</owl:versionInfo>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -1252,7 +1252,6 @@
<!-- http://purl.obolibrary.org/obo/COB_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
- <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Class>
<owl:Axiom>
@@ -1263,14 +1262,6 @@
<sssom:object_label>organism or virus or viroid</sssom:object_label>
<sssom:subject_label>organism</sssom:subject_label>
</owl:Axiom>
- <owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
- <sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
- </owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
@@ -2239,23 +2230,27 @@
- <!-- http://purl.obolibrary.org/obo/NCBITaxon_1 -->
+ <!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ </owl:Class>
<owl:Axiom>
- <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
- <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
- <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<sssom:match_type>HumanCurated</sssom:match_type>
- <sssom:object_label>root</sssom:object_label>
- <sssom:subject_label>organism</sssom:subject_label>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>Viruses</sssom:subject_label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_131567 -->
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_131567">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ </owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000118"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
@@ -2264,6 +2259,14 @@
<sssom:object_label>cellular organisms</sssom:object_label>
<sssom:subject_label>cellular organism</sssom:subject_label>
</owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_131567"/>
+ <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
+ <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
+ <sssom:match_type>HumanCurated</sssom:match_type>
+ <sssom:object_label>organism</sssom:object_label>
+ <sssom:subject_label>cellular organisms</sssom:subject_label>
+ </owl:Axiom>
diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl
index 30e3739..9077f1d 100644
--- a/src/ontology/imports/omo_import.owl
+++ b/src/ontology/imports/omo_import.owl
@@ -12,9 +12,9 @@
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/imports/omo_import.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2021-09-13/imports/omo_import.owl"/>
- <dc:source rdf:resource="http://purl.obolibrary.org/obo/omo/2020-06-08/omo.owl"/>
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-09-13</owl:versionInfo>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/imports/omo_import.owl"/>
+ <dc:source rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2022-04-27/omo.owl"/>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -149,12 +149,14 @@ We also have the outstanding issue of how to aim different definitions to differ
<!-- 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_0000111 xml:lang="en">alternative 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 means the same thing as the preferred name (semantically equivalent)</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.</obo:IAO_0000115>
+ <obo:IAO_0000117>OBO Operations committee</obo:IAO_0000117>
<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:label xml:lang="en">alternative term</rdfs:label>
+ <rdfs:comment>Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).</rdfs:comment>
+ <rdfs:label xml:lang="en">alternative label</rdfs:label>
</owl:AnnotationProperty>
@@ -300,6 +302,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.
<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>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/OMO_0001001"/>
</owl:AnnotationProperty>
@@ -501,6 +504,47 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300]
+ <!-- http://purl.obolibrary.org/obo/OMO_0001001 -->
+
+ <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0001001">
+ <obo:IAO_0000115>This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.</obo:IAO_0000115>
+ <obo:IAO_0000119>OBO Operations call</obo:IAO_0000119>
+ <oboInOwl:created_by rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+ <rdfs:label>logical characteristic of object property</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/OMO_0002000 -->
+
+ <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0002000">
+ <obo:IAO_0000112>'part disjoint with' 'defined by construct' """
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX : <http://example.org/
+ CONSTRUCT {
+ [
+ a owl:Restriction ;
+ owl:onProperty :part_of ;
+ owl:someValuesFrom ?a ;
+ owl:disjointWith [
+ a owl:Restriction ;
+ owl:onProperty :part_of ;
+ owl:someValuesFrom ?b
+ ]
+ ]
+ }
+ WHERE {
+ ?a :part_disjoint_with ?b .
+ }</obo:IAO_0000112>
+ <obo:IAO_0000115>Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.</obo:IAO_0000115>
+ <obo:IAO_0000233 rdf:resource="https://github.com/ontodev/robot/issues/963"/>
+ <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
+ <dc:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+ <rdfs:label>defined by construct</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
<!-- http://purl.org/dc/elements/1.1/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
@@ -609,6 +653,58 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300]
+ <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym">
+ <obo:IAO_0000115>An alternative label for a class or property which has a more general meaning than the preferred name/primary label.</obo:IAO_0000115>
+ <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+ <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/18</obo:IAO_0000233>
+ <rdfs:label xml:lang="en">has broad synonym</rdfs:label>
+ <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/18</rdfs:seeAlso>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+ </owl:AnnotationProperty>
+
+
+
+ <!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
+
+ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
+ <obo:IAO_0000115>An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.</obo:IAO_0000115>
+ <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+ <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/20</obo:IAO_0000233>
+ <rdfs:label xml:lang="en">has exact synonym</rdfs:label>
+ <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/20</rdfs:seeAlso>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+ </owl:AnnotationProperty>
+
+
+
+ <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
+
+ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym">
+ <obo:IAO_0000115>An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.</obo:IAO_0000115>
+ <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+ <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/19</obo:IAO_0000233>
+ <rdfs:label xml:lang="en">has narrow synonym</rdfs:label>
+ <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/19</rdfs:seeAlso>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+ </owl:AnnotationProperty>
+
+
+
+ <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
+
+ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym">
+ <obo:IAO_0000115>An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.</obo:IAO_0000115>
+ <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+ <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/21</obo:IAO_0000233>
+ <rdfs:label xml:lang="en">has related synonym</rdfs:label>
+ <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/21</rdfs:seeAlso>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+ </owl:AnnotationProperty>
+
+
+
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
@@ -700,6 +796,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300]
<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"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMO_0001000"/>
</owl:oneOf>
</owl:Class>
</owl:equivalentClass>
@@ -1224,6 +1321,20 @@ No imports</obo:IAO_0000115>
+ <!-- http://purl.obolibrary.org/obo/OMO_0001000 -->
+
+ <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/OMO_0001000">
+ <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
+ <obo:IAO_0000115 xml:lang="en">The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.</obo:IAO_0000115>
+ <obo:IAO_0000116 xml:lang="en">This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.</obo:IAO_0000116>
+ <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+ <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/77</obo:IAO_0000233>
+ <obo:IAO_0000234>https://orcid.org/0000-0001-5208-3432</obo:IAO_0000234>
+ <rdfs:label>out of scope</rdfs:label>
+ </owl:NamedIndividual>
+
+
+
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
index eac2717..4db91b2 100644
--- a/src/ontology/imports/ro_import.owl
+++ b/src/ontology/imports/ro_import.owl
@@ -16,8 +16,8 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/imports/ro_import.owl">
- <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2021-09-13/imports/ro_import.owl"/>
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-09-13</owl:versionInfo>
+ <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2022-11-02/imports/ro_import.owl"/>
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-11-02</owl:versionInfo>
</owl:Ontology>
@@ -137,6 +137,12 @@
+ <!-- http://purl.obolibrary.org/obo/RO_0002579 -->
+
+ <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002579"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/RO_0002581 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002581">
@@ -279,6 +285,12 @@
+ <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+
+
+
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
@@ -935,6 +947,7 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002131">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
@@ -1004,9 +1017,7 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002578"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002578"/>
</owl:propertyChainAxiom>
- <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
- <obo:IAO_0000115>process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.</obo:IAO_0000115>
- <obo:IAO_0000116>We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit</obo:IAO_0000116>
+ <obo:IAO_0000115>p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000117>David Hill</obo:IAO_0000117>
<obo:IAO_0000117>Tanya Berardini</obo:IAO_0000117>
@@ -1029,7 +1040,7 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002305"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002335"/>
- <obo:IAO_0000115>Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.</obo:IAO_0000115>
+ <obo:IAO_0000115>p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000589>negatively regulates (process to process)</obo:IAO_0000589>
@@ -1053,7 +1064,7 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
</owl:propertyChainAxiom>
- <obo:IAO_0000115>Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.</obo:IAO_0000115>
+ <obo:IAO_0000115>p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000589>positively regulates (process to process)</obo:IAO_0000589>
@@ -1189,6 +1200,7 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002304">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004047"/>
+ <obo:IAO_0000115>p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.</obo:IAO_0000115>
<obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<terms:creator>cjm</terms:creator>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
@@ -1204,9 +1216,11 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002305">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0004046"/>
+ <obo:IAO_0000115>p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.</obo:IAO_0000115>
<obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<terms:creator>cjm</terms:creator>
- <rdfs:comment>holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y</rdfs:comment>
+ <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>causally upstream of, negative effect</rdfs:label>
</owl:ObjectProperty>
@@ -1271,6 +1285,7 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002017"/>
</owl:propertyChainAxiom>
<obo:IAO_0000112>a particular instances of akt-2 enables some instance of protein kinase activity</obo:IAO_0000112>
+ <obo:IAO_0000115>c enables p iff c is capable of p and c acts to execute p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>catalyzes</obo:IAO_0000118>
<obo:IAO_0000118>executes</obo:IAO_0000118>
@@ -1278,7 +1293,6 @@ A continuant cannot have an occurrent as part: use 'participates in'.
<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>
- <obo:IAO_0000232>This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.</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>
@@ -1438,18 +1452,75 @@ A continuant cannot have an occurrent as part: use 'participates in'.
+ <!-- http://purl.obolibrary.org/obo/RO_0002407 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002407">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0012012"/>
+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002407"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002629"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002409"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002409"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002629"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002407"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002629"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002629"/>
+ </owl:propertyChainAxiom>
+ <obo:IAO_0000115>p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.</obo:IAO_0000115>
+ <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
+ <obo:IAO_0000118>indirectly activates</obo:IAO_0000118>
+ <obo:RO_0002579 rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
+ <rdfs:label xml:lang="en">indirectly positively regulates</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/RO_0002409 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002409">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0012012"/>
+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002409"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002630"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002630"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002409"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002630"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002630"/>
+ </owl:propertyChainAxiom>
+ <obo:IAO_0000115>p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.</obo:IAO_0000115>
+ <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
+ <obo:IAO_0000118>indirectly inhibits</obo:IAO_0000118>
+ <obo:RO_0002579 rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
+ <rdfs:label xml:lang="en">indirectly negatively regulates</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
<!-- http://purl.obolibrary.org/obo/RO_0002410 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002410">
- <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_0000115>relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.</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
+ * 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.
@@ -1462,6 +1533,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<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>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002410"/>
+ <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <owl:annotatedTarget>relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.</owl:annotatedTarget>
+ <oboInOwl:hasDbXref>https://en.wikipedia.org/wiki/Causality</oboInOwl:hasDbXref>
+ </owl:Axiom>
@@ -1471,8 +1548,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002418"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
- <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_0000115>p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.</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"/>
@@ -1486,8 +1562,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<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_0000115>p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning 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>
@@ -1501,7 +1576,7 @@ 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_0002501"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002427"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
- <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_0000115>p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of 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>
@@ -1815,7 +1890,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002410"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
- <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_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 where the execution of p influences the execution of q. 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>
@@ -1915,7 +1990,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002578">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002412"/>
- <obo:IAO_0000115>Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.</obo:IAO_0000115>
+ <obo:IAO_0000115>p directly regulates q iff p is immediately causally upstream of q and p regulates 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_0000589>directly regulates (processual)</obo:IAO_0000589>
@@ -2023,7 +2098,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002629">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002213"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
- <obo:IAO_0000115>Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.</obo:IAO_0000115>
+ <obo:IAO_0000115>p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.</obo:IAO_0000115>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000589>directly positively regulates (process to process)</obo:IAO_0000589>
<obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
@@ -2040,7 +2115,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002630">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
- <obo:IAO_0000115>Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.</obo:IAO_0000115>
+ <obo:IAO_0000115>p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.</obo:IAO_0000115>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000589>directly negatively regulates (process to process)</obo:IAO_0000589>
<obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002578"/>
@@ -2271,6 +2346,102 @@ For example, A and B may be gene products and binding of B by A positively regul
+ <!-- http://purl.obolibrary.org/obo/RO_0012011 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0012011">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
+ <obo:IAO_0000115>p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.</obo:IAO_0000115>
+ <oboInOwl:created_by>pg</oboInOwl:created_by>
+ <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-09-26T06:07:17Z</oboInOwl:creation_date>
+ <rdfs:label xml:lang="en">indirectly causally upstream of</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/RO_0012012 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0012012">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0012011"/>
+ <obo:IAO_0000115>p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.</obo:IAO_0000115>
+ <oboInOwl:created_by>pg</oboInOwl:created_by>
+ <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-09-26T06:08:01Z</oboInOwl:creation_date>
+ <rdfs:label xml:lang="en">indirectly regulates</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/RO_0017001 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0017001">
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002233"/>
+ </owl:propertyChainAxiom>
+ <obo:IAO_0000112>A diagnostic testing device utilizes a specimen.</obo:IAO_0000112>
+ <obo:IAO_0000115>X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.</obo:IAO_0000115>
+ <obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899</obo:IAO_0000117>
+ <obo:IAO_0000117>https://orcid.org/0000-0003-2620-0345</obo:IAO_0000117>
+ <obo:IAO_0000232>A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.</obo:IAO_0000232>
+ <obo:IAO_0000232>See github ticket https://github.com/oborel/obo-relations/issues/497</obo:IAO_0000232>
+ <oboInOwl:creation_date>2021-11-08T12:00:00Z</oboInOwl:creation_date>
+ <oboInOwl:hasBroadSynonym>utilizes</oboInOwl:hasBroadSynonym>
+ <rdfs:label xml:lang="en">device utilizes material</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/RO_0019000 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019000">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002410"/>
+ <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002211"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019000"/>
+ </owl:propertyChainAxiom>
+ <obo:IAO_0000115>A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.</obo:IAO_0000115>
+ <terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+ <rdfs:label>regulates characteristic</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/RO_0019001 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019001">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0019000"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002213"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019001"/>
+ </owl:propertyChainAxiom>
+ <obo:IAO_0000115>A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.</obo:IAO_0000115>
+ <terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+ <rdfs:label>positively regulates characteristic</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/RO_0019002 -->
+
+ <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019002">
+ <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0019000"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019001"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002213"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0019002"/>
+ </owl:propertyChainAxiom>
+ <obo:IAO_0000115>A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.</obo:IAO_0000115>
+ <terms:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+ <rdfs:label>negatively regulates characteristic</rdfs:label>
+ </owl:ObjectProperty>
+
+
+
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
@@ -2506,6 +2677,14 @@ For example, A and B may be gene products and binding of B by A positively regul
+ <!-- http://purl.obolibrary.org/obo/CHEBI_50906 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_50906">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CL_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000000">
@@ -2714,13 +2893,22 @@ For example, A and B may be gene products and binding of B by A positively regul
<rdf:Description rdf:about="urn:swrl#mf2">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
+ <rdf:Description rdf:about="urn:swrl:var#p">
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
+ </rdf:Description>
+ <rdf:Description rdf:about="urn:swrl:var#q">
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
+ </rdf:Description>
+ <rdf:Description rdf:about="urn:swrl:var#x">
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
+ </rdf:Description>
<rdf:Description rdf:about="urn:swrl:var#y">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
<rdf:Description rdf:about="urn:swrl:var#z">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
- <rdf:Description rdf:about="urn:swrl:var#x">
+ <rdf:Description rdf:about="urn:swrl:var#u">
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Variable"/>
</rdf:Description>
<rdf:Description>
@@ -3720,6 +3908,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase
</rdf:Description>
</swrl:head>
</rdf:Description>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+ <swrl:body>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#p"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#q"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0012011"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#p"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#q"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+ </rdf:Description>
+ </rdf:rest>
+ </rdf:Description>
+ </swrl:body>
+ <swrl:head>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0012012"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#p"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#q"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+ </rdf:Description>
+ </swrl:head>
+ </rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
@@ -3808,6 +4040,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase
</rdf:Description>
</swrl:head>
</rdf:Description>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+ <swrl:body>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#y"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0019002"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#y"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+ </rdf:Description>
+ </rdf:rest>
+ </rdf:Description>
+ </swrl:body>
+ <swrl:head>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0019001"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#x"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#z"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+ </rdf:Description>
+ </swrl:head>
+ </rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
@@ -3852,6 +4128,50 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase
</rdf:Description>
</swrl:head>
</rdf:Description>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
+ <swrl:body>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#p"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#q"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#q"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#u"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+ </rdf:Description>
+ </rdf:rest>
+ </rdf:Description>
+ </swrl:body>
+ <swrl:head>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
+ <rdf:first>
+ <rdf:Description>
+ <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
+ <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0012011"/>
+ <swrl:argument1 rdf:resource="urn:swrl:var#p"/>
+ <swrl:argument2 rdf:resource="urn:swrl:var#u"/>
+ </rdf:Description>
+ </rdf:first>
+ <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
+ </rdf:Description>
+ </swrl:head>
+ </rdf:Description>
</rdf:RDF>