Merge pull request #152 from obophenotype/update

New release
obophenotype · Sep 15, 2022 · a7757e0 · a7757e0
2 parents b5e7893 + 99a30b5
commit a7757e0
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Showing 84 changed files with 499,545 additions and 5,302,289 deletions.
diff --git a/.gitignore b/.gitignore
@@ -50,3 +50,12 @@ src/patterns/reserved_iris.txt
 src/patterns/tmp
 src/patterns/xpo.csv
 src/ontology/reports/trailing-whitespace-violation.csv
+xpo-full.json
+xpo-full.obo
+xpo-full.owl
+xpo-simple.json
+xpo-simple.obo
+xpo-simple.owl
+xpo.json
+xpo.obo
+xpo.owl
diff --git a/patterns/definitions.owl b/patterns/definitions.owl
diff --git a/patterns/pattern.owl b/patterns/pattern.owl
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -10,9 +10,9 @@
      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/xpo/imports/bfo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/bfo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/bfo_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
@@ -10,8 +10,8 @@
      xmlns:chebi="http://purl.obolibrary.org/obo/chebi#3"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/xpo/imports/chebi_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/chebi_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/chebi_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl
diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl
@@ -10,9 +10,9 @@
      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/xpo/imports/iao_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/iao_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/iao_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -874,6 +874,30 @@ Previous. An information content entity is a non-realizable information entity t
 
 
 
+    <!-- http://purl.obolibrary.org/obo/PATO_0000125 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000125">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001018"/>
+        <obo:IAO_0000111>mass</obo:IAO_0000111>
+        <obo:IAO_0000115>A physical quality that inheres in a bearer by virtue of the proportion of the bearer&apos;s amount of matter.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
+        <rdfs:label>mass</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/PATO_0001018 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001018">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001241"/>
+        <obo:IAO_0000111>physical quality</obo:IAO_0000111>
+        <obo:IAO_0000115>A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
+        <rdfs:label>physical quality</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/PATO_0001241 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001241">

diff --git a/src/ontology/imports/nbo_import.owl b/src/ontology/imports/nbo_import.owl
@@ -19,9 +19,9 @@
      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/xpo/imports/nbo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/nbo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/nbo_import.owl"/>
         <dc:source rdf:resource="http://purl.obolibrary.org/obo/nbo/releases/2021-02-15/nbo.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -498,7 +498,9 @@
 
     <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym">
+        <rdfs:label>has_narrow_synonym</rdfs:label>
+    </owl:AnnotationProperty>
 
 
 
@@ -2926,7 +2928,7 @@ For example, A and B may be gene products and binding of B by A positively regul
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0009605"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hb</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>GOC:hb</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -2947,7 +2949,7 @@ For example, A and B may be gene products and binding of B by A positively regul
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0009612"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hb</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>GOC:hb</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -2971,7 +2973,7 @@ For example, A and B may be gene products and binding of B by A positively regul
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0009628"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hb</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>GOC:hb</oboInOwl:hasDbXref>
     </owl:Axiom>
 
 
@@ -3834,7 +3836,7 @@ For example, A and B may be gene products and binding of B by A positively regul
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PATO_0000161"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>A quality of a single process inhering in a bearer by virtue of the bearer&apos;s occurrence per unit time.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PATOC:melissa</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>PATOC:melissa</oboInOwl:hasDbXref>
     </owl:Axiom>