Merge pull request #304 from OBOFoundry/update-complex-of-molecules

jamesaoverton · web-flow · commit 6e206cdf60bc · 2025-06-30T11:14:11.000-04:00
Minor edit to 'complex of molecules'
diff --git a/cob-base.owl b/cob-base.owl
@@ -10,12 +10,12 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      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/2025-02-20/cob-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-06-12/cob-base.owl"/>
         <dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
         <terms:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</terms:description>
         <terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
         <terms:title xml:lang="en">Core Ontology for Biology and Biomedicine</terms:title>
-        <owl:versionInfo>2025-02-20</owl:versionInfo>
+        <owl:versionInfo>2025-06-12</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -418,7 +418,7 @@
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A complex of two or more molecular entities that are not covalently bound.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A complex of two or more molecules that are not covalently bound.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">complex of molecules</rdfs:label>
     </owl:Class>
     
diff --git a/cob-root.owl b/cob-root.owl
@@ -9,11 +9,11 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      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/2025-02-20/cob-root.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-06-12/cob-root.owl"/>
         <terms:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</terms:description>
         <terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
         <terms:title xml:lang="en">Core Ontology for Biology and Biomedicine</terms:title>
-        <owl:versionInfo>2025-02-20</owl:versionInfo>
+        <owl:versionInfo>2025-06-12</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -714,7 +714,7 @@
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A complex of two or more molecular entities that are not covalently bound.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A complex of two or more molecules that are not covalently bound.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">complex of molecules</rdfs:label>
     </owl:Class>
     
diff --git a/cob.owl b/cob.owl
@@ -9,11 +9,11 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      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/2025-02-20/cob.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2025-06-12/cob.owl"/>
         <terms:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</terms:description>
         <terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
         <terms:title xml:lang="en">Core Ontology for Biology and Biomedicine</terms:title>
-        <owl:versionInfo>2025-02-20</owl:versionInfo>
+        <owl:versionInfo>2025-06-12</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -704,7 +704,7 @@
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:IAO_0000115 xml:lang="en">A complex of two or more molecular entities that are not covalently bound.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A complex of two or more molecules that are not covalently bound.</obo:IAO_0000115>
         <rdfs:label xml:lang="en">complex of molecules</rdfs:label>
     </owl:Class>
     
diff --git a/cob.tsv b/cob.tsv
@@ -27,7 +27,7 @@ COB:0000049	nucleic acid chain	A molecule that consists of nucleotides (unmodifi
 COB:0000056	obsolete immaterial anatomical entity					
 COB:0000073	obsolete gene product					
 COB:0000077	obsolete action specification					
-COB:0000080	complex of molecules	A complex of two or more molecular entities that are not covalently bound.	BFO:0000040	material entity	BFO:0000051 some COB:0000013	has part some molecule
+COB:0000080	complex of molecules	A complex of two or more molecules that are not covalently bound.	BFO:0000040	material entity	BFO:0000051 some COB:0000013	has part some molecule
 COB:0000082	planned process	A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.	BFO:0000015	process		
 COB:0000083	failed planned process		COB:0000082	planned process		
 COB:0000110	material processing	A planned process that intends to output material entities from input material entities	COB:0000035	completely executed planned process	(OBI:0000293 some BFO:0000040) and (OBI:0000299 some BFO:0000040)	(has specified input some material entity) and (has specified output some material entity)
diff --git a/src/ontology/cob-edit.tsv b/src/ontology/cob-edit.tsv
@@ -44,7 +44,7 @@ PR:000000001	protein	owl:Class	An amino acid chain that is produced de novo by r
 SO:0000110	sequence_feature	owl:Class	Any extent of continuous biological sequence.		ROOT	root of Sequence Ontology	material entity										COB injects: subclass of 'material entity'
 SO:0001060	sequence_variant	owl:Class	A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.		ROOT	root of Sequence Ontology	material entity										COB injects: subclass of 'material entity'
 SO:0001260	sequence_collection	owl:Class	A collection of discontinuous sequences.		ROOT	root of Sequence Ontology	material entity										COB injects: subclass of 'material entity'
-COB:0000080	complex of molecules	owl:Class	A complex of two or more molecular entities that are not covalently bound.		BASE		material entity	'has material part' some 'molecule'									
+COB:0000080	complex of molecules	owl:Class	A complex of two or more molecules that are not covalently bound.		BASE		material entity	'has material part' some 'molecule'									
 GO:0032991	protein-containing complex	owl:Class	A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.	This is not covalently bonded, which conflicts with changes to the parent definition.	FULL	member of 'cellular component' root group union	complex of molecules	'has material part' some protein									
 GO:0044423	virion component	owl:Class	Any constituent part of a virion, a complete fully infectious extracellular virus particle.		ROOT GROUP: MEMBER	member of 'cellular component' root group union	material entity										
 GO:0110165	cellular anatomical entity	owl:Class	A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.	Overlaps with some cellular components from GO|Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes.	FULL	member of 'cellular component' root group union	material entity	'has material part' some 'molecule'									
diff --git a/src/ontology/imports/DRON_import.owl b/src/ontology/imports/DRON_import.owl
@@ -57,8 +57,8 @@
     <!-- http://purl.obolibrary.org/obo/DRON_00000005 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DRON_00000005">
-        <rdfs:label xml:lang="en">drug product</rdfs:label>
-        <obo:IAO_0000115 xml:lang="en">a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">clinical drug product</rdfs:label>
+        <obo:IAO_0000115 xml:lang="en">A drug product that is bearer of a clinical drug role.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/dron.owl"/>
     </owl:Class>
 </rdf:RDF>
diff --git a/src/ontology/imports/PR_import.owl b/src/ontology/imports/PR_import.owl
@@ -54,7 +54,7 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/PR_000000001">
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein</rdfs:label>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.</obo:IAO_0000115>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pr.owl"/>
     </owl:Class>
     
@@ -64,7 +64,7 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/PR_000018263">
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">amino acid chain</rdfs:label>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.</obo:IAO_0000115>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A molecule that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pr.owl"/>
     </owl:Class>
 </rdf:RDF>
diff --git a/src/ontology/imports/RO_import.owl b/src/ontology/imports/RO_import.owl
@@ -98,7 +98,7 @@
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
         <rdfs:label xml:lang="en">is concretized as</rdfs:label>
-        <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
     </owl:ObjectProperty>
     
@@ -108,7 +108,7 @@
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
         <rdfs:label xml:lang="en">concretizes</rdfs:label>
-        <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
     </owl:ObjectProperty>
     
