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 ***@***.***> wrote: 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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=AAAMMOKREYDXMPAG7A3P5M3QIZ2AZA5CNFSM4IU5KQ72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6IGT7A#issuecomment-529558012>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAAMMOPPK6MP6VJTZPWVMULQIZ2AZANCNFSM4IU5KQ7Q> .