remove --axioms external is removing transitivity axioms from in-base properties

[gouttegd]

When using robot remove --base-iri <BASE_IRI> --axioms external to remove axioms relative to “external” entities (entities that are not in the <BASE_IRI> namespace), all object properties within the base IRI namespace lose their transitive characteristic.

Minimal example to reproduce:

Prefix(owl:=<http://www.w3.org/2002/07/owl#>)

Ontology(<http://example.org/untitled-ontology/>

Declaration(ObjectProperty(<http://example.org/UO_0001>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000589>))

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000589> <http://example.org/UO_0001> "example_property"@en)
TransitiveObjectProperty(<http://example.org/UO_0001>)
SubObjectPropertyOf(<http://example.org/UO_0001> owl:topObjectProperty)

)

Observe that the http://example.org/UO_0001 property is declared to be transitive.

Using the following command to remove any entity outside of the http://example.org/UO_ namespace:

$ robot remove -i input.ofn --base-iri http://example.org/UO_ --axioms external -o output.ofn

yields an output ontology where the http://example.org/UO_0001 property is still present (as expected since it belongs to the specified base IRI namespace) but is no longer transitive:

Prefix(owl:=<http://www.w3.org/2002/07/owl#>)

Ontology(<http://example.org/untitled-ontology/>

Declaration(ObjectProperty(<http://example.org/UO_0001>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000589>))

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000589> <http://example.org/UO_0001> "example_property"@en)
SubObjectPropertyOf(<http://example.org/UO_0001> owl:topObjectProperty)

)

As explicitly confirmed by a robot diff:

$ robot diff --left input.ofn --right output.ofn
1 axioms in left ontology but not in right ontology:
- TransitiveObjectProperty(<http://example.org/UO_0001>)

0 axioms in right ontology but not in left ontology:

[gouttegd]

Observed with ROBOT-1.9.1, ROBOT-1.9.2, and with a locally built version from the tip of the master branch as of March 28.

[matentzn]

I remember this issue from long ago, and I think I know how to fix it.

[matentzn]

Ok this is constituted the last major issue on my ODK testing spree. It is not a disaster, but for ontologies that coin object property characteristics and axioms (including domain/range!), they will never be included in the base release until this is fixed.

I have put in hotfix for RO (oborel/obo-relations#793) for now, and anyone who is harmed by that issue can feel free to do the same.