Help needed: oboInOwl spec vs obographs

[matentzn]

I need a recommendation of what to do when people physically include the oboinowl ontology in their ontology; can I safely recommend to remove it in all cases?

The reason I am posting this here is that running

robot -vvv convert -I http://www.geneontology.org/formats/oboInOwl -f json -o out.json

causes #49

And I dont understand whether this is intentional (i.e. oboinowl ontology is somehow broken) or whether this is a limitation of obographs.. Thanks for the help! @dosumis @cmungall

[matentzn]

I guess the problem must be this:

<oboInOwl:hasDefinition>
      <oboInOwl:Definition>
        <rdfs:label xml:lang="en">An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle</rdfs:label>
        <oboInOwl:hasDbXref>
          <oboInOwl:DbXref>
            <rdfs:label>oboInOwl:GOC</rdfs:label>
            <oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC</oboInOwl:hasURI>
          </oboInOwl:DbXref>
        </oboInOwl:hasDbXref>
      </oboInOwl:Definition>
    </oboInOwl:hasDefinition>

While oboInOwl:hasDefinition is an annotation property.. Not really allowed in RDF i assume.

[cmungall]

Never include it. It predates OWL2. In the new OBO OM we should redefine the PURLs.

On Mon, Sep 9, 2019 at 9:29 AM Nico Matentzoglu notifications@github.com wrote:

I guess the problem must be this:

An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle oboInOwl:GOC http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC While oboInOwl:hasDefinition is an annotation property.. Not really allowed in RDF i assume. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or mute the thread .