Multiple definitions failure is too strict?

[bjonnh]

I was trying to import some terms from ENVO using the ontology-starter-kit.

Owltools fail converting that to OBO. (see the issue I submitted for owltools) : owlcollab/owltools#248

In ENVO, IAO and BFO, terms have multiple IAO_0000115 (definition), one being annotated as being an axiom.

So my question here is: Is OWLAPI too strict here?

[ignazio1977]

It might be that this is too strict in real life applications, however this is part of the OBO specs so it needs OBO experts to weigh in. @cmungall what do you think?

[cmungall]

This can be switched off with setCheckStructure(false), in which case behavior with multiple text defs is undefined after roundtripping (one will text def will be dropped).

I followed up on your ticket here:
owlcollab/owltools#248

Both owltools and robot now have commands to pass in an override to strict mode on the command line.

I'll follow up with @pbuttigieg to fix ENVO as this shouldn't be happening. Regardless of the format used, we should have a single text definition. This can be violated either by accident or by superimposing different versions of the same ontology through stale imports. Previously the only check we have against this was the obo conversion, but in the next release of robot we'll have sparql checks so that people get this QC regardless of conversion.

[bjonnh]

Thanks, I switched to robot in my makefiles (not everywhere yet though).