Merge pull request #480 from obophenotype/issue-467-fix-ns

namespace and def APs were inverted. Fixed.
obophenotype · Jul 22, 2017 · f00bd8b · f00bd8b
2 parents f74f3a0 + 37a2fb2
commit f00bd8b
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -105,8 +105,10 @@ MIRROR_TRIGGER =
 
 # clone remote ontology locally, perfoming some excision of relations and annotations
 # Note: use .obo for faster download
-mirror/%.owl: $(MIRROR_TRIGGER)
-	owltools $(OBO)/$*.obo --remove-annotation-assertions -l --remove-dangling-annotations --make-subset-by-properties -f $(KEEPRELS)  -o $@
+mirror/%.obo: $(MIRROR_TRIGGER)
+	wget --no-check-certificate $(OBO)/$*.obo -O $@
+mirror/%.owl: mirror/%.obo
+	owltools $< --remove-annotation-assertions -l --remove-dangling-annotations --make-subset-by-properties -f $(KEEPRELS)  -o $@
 mirror/uberon.owl: $(MIRROR_TRIGGER)
 	owltools $(OBO)/uberon.owl --remove-annotation-assertions -l -s -d --remove-axiom-annotations --remove-dangling-annotations --make-subset-by-properties -n $(KEEPRELS) --set-ontology-id $(OBO)/uberon.owl -o $@
 mirror/pr.obo: 

diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -13226,11 +13226,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0001070> ObjectSomeValuesFrom(<htt
 
 # Class: <http://purl.obolibrary.org/obo/CL_0001071> (group 3 innate lymphoid cell)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0001071> "cell")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CL_0001071> "cell")
 AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/CL_0001071> <http://orcid.org/0000-0001-9990-8331>)
 AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/CL_0001071> "2017-01-31T20:21:26Z"^^xsd:dateTime)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0001071> "ILC3")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:add") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:dsd") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:23292121") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:23348417") <http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CL_0001071> "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:add") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:dsd") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:23292121") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:23348417") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0001071> "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0001071> "group 3 innate lymphoid cell")
 EquivalentClasses(<http://purl.obolibrary.org/obo/CL_0001071> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CL_0001065> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/PR_000003455>)))
 SubClassOf(<http://purl.obolibrary.org/obo/CL_0001071> <http://purl.obolibrary.org/obo/CL_0001065>)
@@ -26516,4 +26516,4 @@ SubClassOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <htt
 SubClassOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0001908>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0005634>))
 SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000050>) <http://purl.obolibrary.org/obo/BFO_0000066>)
 SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/RO_0002211> <http://purl.obolibrary.org/obo/BFO_0000050>) <http://purl.obolibrary.org/obo/RO_0002211>)
-)
+)
diff --git a/src/ontology/mirror/README.md b/src/ontology/mirror/README.md
@@ -0,0 +1 @@
+This folder is used by the release process to stage external ontologies
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This folder is used by the release process to stage external ontologies