Merge pull request #247 from OBOFoundry/release16112023

Update COB release (nucleic acid / electron fix)
OBOFoundry · Jan 25, 2024 · 0c62f74 · 0c62f74
2 parents 3249854 + dc45899
commit 0c62f74
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Showing 10 changed files with 533 additions and 505 deletions.
diff --git a/cob-base-reasoned.owl b/cob-base-reasoned.owl
diff --git a/cob-base.owl b/cob-base.owl
diff --git a/cob-examples-reasoned.owl b/cob-examples-reasoned.owl
diff --git 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/2023-05-12/cob-full.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-11-16/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>2023-05-12</owl:versionInfo>
+        <owl:versionInfo>2023-11-16</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -812,7 +812,7 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000049">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
-        <obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_10545</obo:COB_based_on>
+        <obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_33696</obo:COB_based_on>
         <rdfs:label>nucleic acid polymer</rdfs:label>
     </owl:Class>
 
@@ -1458,5 +1458,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a
 
 
 
-<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git 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/2023-05-12/cob-native.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-11-16/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>2023-05-12</owl:versionInfo>
+        <owl:versionInfo>2023-11-16</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -1387,5 +1387,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a
 
 
 
-<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/cob.owl b/cob.owl
@@ -9,14 +9,14 @@
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:skos="http://www.w3.org/2004/02/skos/core#"
-     xmlns:terms="http://purl.org/dc/terms/">
+     xmlns:dcterms="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/2023-05-12/cob.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-11-16/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/"/>
+        <dcterms: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>2023-05-12</owl:versionInfo>
+        <owl:versionInfo>2023-11-16</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -529,15 +529,13 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_10545">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36342"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000801"/>
                 <owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
             </owl:Restriction>
         </rdfs:subClassOf>
         <rdfs:label xml:lang="en">electron</rdfs:label>
-        <rdfs:label>nucleic acid polymer</rdfs:label>
     </owl:Class>
 
 
@@ -590,6 +588,15 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHEBI_33696 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33696">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
+        <rdfs:label>nucleic acid polymer</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/CHEBI_36342 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36342">
@@ -1381,5 +1388,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a
 
 
 
-<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/cob.tsv b/cob.tsv
@@ -11,12 +11,13 @@ BFO:0000141	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		
-CHEBI:10545	electron		CHEBI:36342|COB:0000013	molecular entity|subatomic particle	COB:0000801 value 0	has number of atomic nuclei value 0
+CHEBI:10545	electron		CHEBI:36342	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		
 CHEBI:30222	neutron		CHEBI:36342	subatomic particle		
 CHEBI:33250	uncharged atom		COB:0000011	atom		
 CHEBI:33252	atomic nucleus		CHEBI:36342	subatomic particle		
+CHEBI:33696	nucleic acid polymer		COB:0000013	molecular entity		
 CHEBI:36342	subatomic particle		BFO:0000040	material entity		
 CL:0000000	cell	A material entity that has a plasma membrane and results from cellular division.	BFO:0000040	material entity		
 CL:0000003	native cell		CL:0000000	cell		

diff --git a/src/ontology/cob.Makefile b/src/ontology/cob.Makefile
@@ -87,7 +87,7 @@ cob.tsv: cob.owl
 #
 
 $(TMPDIR)/cob-to-external.sssom.owl: $(COMPONENTSDIR)/cob-to-external.tsv | $(TMPDIR)
-	sssom convert $< -o $@
+	sssom convert $< --output-format owl -o $@
 
 $(COB_TO_EXTERNAL): $(TMPDIR)/cob-to-external.sssom.owl
 	$(ROBOT) merge -i $< \

diff --git a/src/ontology/components/cob-annotations.owl b/src/ontology/components/cob-annotations.owl
@@ -9,7 +9,7 @@
      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>2023-05-12</owl:versionInfo>
+        <owl:versionInfo>2023-11-16</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -116,7 +116,7 @@
         <obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_33250</obo:COB_based_on>
     </rdf:Description>
     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000049">
-        <obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_10545</obo:COB_based_on>
+        <obo:COB_based_on>http://purl.obolibrary.org/obo/CHEBI_33696</obo:COB_based_on>
     </rdf:Description>
     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000055">
         <obo:COB_based_on>http://purl.obolibrary.org/obo/PCO_0000000</obo:COB_based_on>
@@ -214,5 +214,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->