SPARQL taxon expansion does nothing

[matentzn]

Right now the goal to generate the intermediate uberon (processed version) looks like this:

$(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(SCRIPTSDIR)/expand-dbxref-literals.pl
	echo "STRONG WARNING: issues/contributor.owl needs to be manually updated."
	$(OWLTOOLS) --no-logging $< $(COMPONENTSDIR)/disjoint_union_over.ofn issues/contributor.owl --merge-support-ontologies --expand-macros -o  $@ &&  $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > [email protected]
	# The previous step seems to be necessary because somehow the expand-dbxref-literals script expects the owtools output.. No idea why
	$(ROBOT) merge -i [email protected] \
		query \
			--update $(SPARQLDIR)/taxon_constraint_never_in_taxon.ru \
			--update $(SPARQLDIR)/remove_axioms.ru \
			--update $(SPARQLDIR)/delete-definition-dot.ru \
		merge -i imports/ro_import.owl -o $@

--expand-macros

Not only adds the correct Disjointness axioms, it also removes the annotations that are being expanded. So, before

--update $(SPARQLDIR)/taxon_constraint_never_in_taxon.ru 

kicks in, the never_in_taxon has already been dropped: so it does nothing.

This ticket should be part of the great makefile revision. Maye we add a tag for that process @shawntanzk?

[balhoff]

Let's get this moving along: https://github.com/ontodev/robot/pull/964

I think I need to update the annotation property IRI with the one you added to OMO.

[matentzn]

Yeah agree.. If you change the IRI I will review the PR again, and get James to take a look as well.

[matentzn]

This also leads to never_in_taxon annotations entirely disappearing from the release files (their expansions are there, however).

[shawntanzk]

@balhoff - might need your help with this, could you help by giving an example of expand here please? thanks :)

[balhoff]

@shawntanzk https://github.com/oborel/obo-relations/pull/616

To make that work, we need to merge that PR, make an RO release, refresh Uberon RO import, update to ODK v1.3.1, add expand into Uberon ROBOT chains somewhere. I think we will want to run all expansions for QC, but suppress 'present in taxon' for release output (there is an argument for that).

[anitacaron]

• [x] merge that PR
• [x] make a RO release - https://github.com/oborel/obo-relations/pull/617
• [x] refresh Uberon RO import - https://github.com/obophenotype/uberon/pull/2575
• [x] update to ODK v1.3.1
• [x] add expand into Uberon ROBOT chains somewhere

[matentzn]

http://robot.obolibrary.org/expand