repair --merge-axiom-annotations is removing axioms it shouldn’t remove #1239
Description
I believe there are two (maybe related) problems with the repair --merge-axiom-annotations feature.
They can both be illustrated with the following minimal example:
Ontology(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>
# Declarations omitted for brevity...
# Object Property: <http://purl.obolibrary.org/obo/RO_0001025> (located in)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0001025> "located in")
ObjectPropertyDomain(Annotation(<http://purl.obolibrary.org/obo/IAO_0000116> "Some annotation.") <http://purl.obolibrary.org/obo/RO_0001025> <http://purl.obolibrary.org/obo/BFO_0000004>)
ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0001025> ObjectComplementOf(<http://purl.obolibrary.org/obo/BFO_0000006>))
# Class: <http://purl.obolibrary.org/obo/GO_0005319> (lipid transporter activity)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0005319> "lipid transporter activity")
SubClassOf(<http://purl.obolibrary.org/obo/GO_0005319> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/GO_0006869>))
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "GO_REF:0000090") <http://purl.obolibrary.org/obo/GO_0005319> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/GO_0006869>))
)
Running robot repair -i minimal.ofn --merge-axiom-annotations true -o repaired.ofn yields
Ontology(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>
# Declarations omitted for brevity...
# Object Property: <http://purl.obolibrary.org/obo/RO_0001025> (located in)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0001025> "located in")
ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0001025> ObjectComplementOf(<http://purl.obolibrary.org/obo/BFO_0000006>))
# Class: <http://purl.obolibrary.org/obo/GO_0005319> (lipid transporter activity)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0005319> "lipid transporter activity")
SubClassOf(<http://purl.obolibrary.org/obo/GO_0005319> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/GO_0006869>))
)
The first problem is with the RO:0001025 property: note how the following axiom
ObjectPropertyDomain(Annotation(http://purl.obolibrary.org/obo/IAO_0000116 "Some annotation.") http://purl.obolibrary.org/obo/RO_0001025 http://purl.obolibrary.org/obo/BFO_0000004)
is completely removed.
The second problem is with the GO:0005319 class. The original file contains the same axiom (GO:0005319 SubClassOf BFO:0000050 some GO:0006869) twice: one unannotated, one carrying a GO_REF:0000090 cross-reference annotation. After “repair”, the annotated axiom is completely removed, meaning the cross-reference annotation is lost. This is not the behaviour I would expect for --merge-axiom-annotations -- I would have the annotation to be preserved, and the unannotated axiom to be removed.