Unable to import ncbitaxon taxslim-disjoint-over-in-taxon.owl

[gaurav]

When running ROBOT_JAVA_ARGS="-Xmx96G -XX:+UseParallelGC" robot mirror -i ontologies.ofn -d mirror -o mirror/catalog-v001.xml in https://github.com/ExposuresProvider/cam-pipeline/pull/98, I get the following error:

org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl> Cause: Ontology already exists. OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl>) VersionIRI(<http://purl.obolibrary.org/obo/ncbitaxon/releases/2023-06-16/subsets/taxslim.owl>))

This appears to be because both of those ontologies are identified with the identifier http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl.

Comparing those files, it looks like they are identical exception for one additional RO term in http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl. Since this is the case, I will comment out http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl for now. But we might want to contact ncbitaxon and figure out which of these files we should use.

[balhoff]

@gaurav this is a temporary issue that I reported earlier today: https://github.com/obophenotype/ncbitaxon/issues/76

[gaurav]

@balhoff Nice! I've added a note to https://github.com/ExposuresProvider/cam-pipeline/pull/100 so we wait for that bug to be fixed upstream before updating and merging that PR.

[anitacaron]

Hi @gaurav, there's a new release fixing this issue. You can try your pipeline again.

[gaurav]

Thanks, @anitacaron, this works now! Closed in PR #100.