From 8aca42d2bb50ba764982788e257c1fd2f6f8c878 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Wed, 14 Aug 2024 10:31:13 +0300
Subject: [PATCH] Adding a fix to VBO release pipeline that ensures OBO
 conversion is always possible

See https://github.com/OBOFoundry/COB/issues/229

AGAIN.. GRRR.
---
 src/ontology/imports/cob_import.owl |  6 ++----
 src/ontology/vbo.Makefile           | 13 +++++++++++++
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl
index c10322d..a85414f 100644
--- 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/vbo/imports/cob_import.owl>
-<http://purl.obolibrary.org/obo/vbo/releases/2024-08-08/imports/cob_import.owl>
+<http://purl.obolibrary.org/obo/vbo/releases/2024-08-14/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 "2024-08-08")
+Annotation(owl:versionInfo "2024-08-14")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
@@ -167,7 +167,6 @@ 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(Annotation(rdfs:comment "We should name the inverse in COB and avoid the confusing inverse(..) construct") <http://purl.obolibrary.org/obo/BFO_0000020> ObjectSomeValuesFrom(ObjectInverseOf(<http://purl.obolibrary.org/obo/RO_0000053>) owl:Thing))
 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)
@@ -294,7 +293,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000027> <http://purl.obolibrary.
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IAO_0000030> "Pier: 'data, information or knowledge'. OR 'representation")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000030> "information")
 SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000030> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/IAO_0000136> owl:Thing))
-SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000030> ObjectSomeValuesFrom(ObjectInverseOf(<http://purl.obolibrary.org/obo/COB_0000078>) <http://purl.obolibrary.org/obo/COB_0000120>))
 
 
 )
\ No newline at end of file
diff --git a/src/ontology/vbo.Makefile b/src/ontology/vbo.Makefile
index 37965c6..e7d842b 100644
--- a/src/ontology/vbo.Makefile
+++ b/src/ontology/vbo.Makefile
@@ -110,6 +110,19 @@ $(IMPORTDIR)/wikidata_import.owl: $(TMPDIR)/wikidata_labels.ttl
 .PHONY: wikidata
 wikidata: $(IMPORTDIR)/wikidata_import.owl
 
+# The below fix basically deals with a longstanding issue that the OBO format converter does not handle the 
+# ObjectInverseOf axiom. This is a workaround until the issue is fixed in the OBO format converter
+# https://github.com/OBOFoundry/COB/issues/229
+
+.PHONY: mirror-cob
+.PRECIOUS: $(MIRRORDIR)/cob.owl
+mirror-cob: | $(TMPDIR)
+	curl -L $(OBOBASE)/cob.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/cob-download.owl -f ofn -o $(TMPDIR)/$@.owl && \
+	sed -i '/ObjectInverseOf/d' $(TMPDIR)/$@.owl
+
+
+
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