Remove logical axioms from COB import related to RO properties (#798)

* remove logical axioms from cob import related to ro properties * remove also annotations in cob imports --------- Co-authored-by: Anita Caron <[email protected]>
oborel · Apr 22, 2024 · 56e283c · 56e283c
1 parent f0994da
commit 56e283c
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diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>
-<http://purl.obolibrary.org/obo/ro/releases/2024-03-02/imports/cob_import.owl>
+<http://purl.obolibrary.org/obo/ro/releases/2024-04-05/imports/cob_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl>)
-Annotation(owl:versionInfo "2024-03-02")
+Annotation(owl:versionInfo "2024-04-05")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
@@ -20,12 +20,12 @@ Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000070>))
 Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000121>))
 Declaration(Class(<http://purl.obolibrary.org/obo/COB_0001000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003674>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005634>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000070>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000054>))
@@ -58,45 +58,14 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "def
 #   Object Properties
 ############################
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (<http://purl.obolibrary.org/obo/BFO_0000050>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051>)
-TransitiveObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>)
-
 # Object Property: <http://purl.obolibrary.org/obo/BFO_0000054> (realized in)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000054> "realized in"@en)
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000066> (<http://purl.obolibrary.org/obo/BFO_0000066>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000067>)
-ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000015>)
-
 # Object Property: <http://purl.obolibrary.org/obo/BFO_0000067> (contains process)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000067> "contains process"@en)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (<http://purl.obolibrary.org/obo/RO_0000052>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/RO_0000053>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000053> (<http://purl.obolibrary.org/obo/RO_0000053>)
-
-InverseFunctionalObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>)
-ObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/BFO_0000020>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000056> (<http://purl.obolibrary.org/obo/RO_0000056>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/RO_0000057>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000057> (<http://purl.obolibrary.org/obo/RO_0000057>)
-
-ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/BFO_0000015>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0002333> (<http://purl.obolibrary.org/obo/RO_0002333>)
-
-SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002333> <http://purl.obolibrary.org/obo/RO_0000057>)
-
 
 
 ############################
@@ -106,7 +75,6 @@ SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002333> <http://purl.obo
 # Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000015> "process"@en)
-SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000015>))
 
 # Class: <http://purl.obolibrary.org/obo/BFO_0000016> (disposition)
 
@@ -123,7 +91,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000017> <http://purl.obolibrary.
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000020> "characteristic"@en)
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/BFO_0000020> "https://github.com/OBOFoundry/COB/issues/65")
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/BFO_0000020> "https://github.com/oborel/obo-relations/pull/284")
-SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000020> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/BFO_0000020>))
 
 # Class: <http://purl.obolibrary.org/obo/BFO_0000023> (role)
 
@@ -179,7 +146,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0008150> "A biological process is an evolved process")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0008150> "biological process"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/BFO_0000015>)
-SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0003674>))
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000070> (assay)
 

diff --git a/src/ontology/ro.Makefile b/src/ontology/ro.Makefile
@@ -53,7 +53,7 @@ $(IMPORTDIR)/cob_import.owl: $(MIRRORDIR)/cob.owl $(IMPORTDIR)/cob_terms_combine
 	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
     extract -T $(IMPORTDIR)/cob_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
 	remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/cob_terms_combined.txt --select complement \
-	remove --select "RO:* BFO:0000050* BFO:0000051* BFO:0000060* BFO:0000066*" --axioms "annotation" \
+	remove --select "RO:* BFO:0000050* BFO:0000051* BFO:0000060* BFO:0000066*" --axioms "annotation logical" \
 	query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 	$(ANNOTATE_CONVERT_FILE); fi