Conversion from OBO to OWL Functional creates invalid IRIs

[althonos]

Hi!

When converting from OBO to OWL Functional, some prefixed identifiers are expanded without proper escaping, creating the invalid IRIs.

Example:

• Download ecocore.obo
• Run robot convert --input ecocore.obo --format ofn --output ecocore.ofn

The resulting file will contain invalid IRIs such as:

http://www.geneontology.org/formats/oboInOwl#http://www.w3.org/2000/01/rdf-schema#seeAlso

(this is also an obvious roundtrip issue but as far as this goes I'm only concerned about the syntax right now).

Related issues:

• owlcs/owlapi#863
• owlcollab/owltools#286

[cmungall]

ugh! I think the owlapi is the best place for this issue as robot is just a messenger

…

On Fri, Jul 12, 2019 at 2:58 PM Martin Larralde ***@***.***> wrote: Hi! When converting from OBO to OWL Functional, some prefixed identifiers are expanded without proper escaping, creating the invalid IRIs. Example: - Download ecocore.obo <http://purl.obolibrary.org/obo/ecocore.obo> - Run robot convert --input ecocore.obo --format ofn --output ecocore.ofn The resulting file will contain invalid IRIs such as: http://www.geneontology.org/formats/oboInOwl#http://www.w3.org/2000/01/rdf-schema#seeAlso (this is also an obvious roundtrip issue but as far as this goes I'm only concerned about the syntax right now). Related issues: - owlcs/owlapi#863 <owlcs/owlapi#863> - owlcollab/owltools#286 <owlcollab/owltools#286> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#534?email_source=notifications&email_token=AAAMMOIXBHX2WXOT7DYDYW3P7D5AFA5CNFSM4ICSB4G2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G67IEUA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAAMMOIUNFNCY46J2WOZOFTP7D5AFANCNFSM4ICSB4GQ> .

[cmungall]

you might want to file a bug on ecocore and I'll work with them to fix their obo

…

On Fri, Jul 12, 2019 at 4:18 PM Chris Mungall ***@***.***> wrote: ugh! I think the owlapi is the best place for this issue as robot is just a messenger On Fri, Jul 12, 2019 at 2:58 PM Martin Larralde ***@***.***> wrote: > Hi! > > When converting from OBO to OWL Functional, some prefixed identifiers are > expanded without proper escaping, creating the invalid IRIs. > > Example: > > - Download ecocore.obo <http://purl.obolibrary.org/obo/ecocore.obo> > - Run robot convert --input ecocore.obo --format ofn --output > ecocore.ofn > > The resulting file will contain invalid IRIs such as: > > http://www.geneontology.org/formats/oboInOwl#http://www.w3.org/2000/01/rdf-schema#seeAlso > > (this is also an obvious roundtrip issue but as far as this goes I'm only > concerned about the syntax right now). > > Related issues: > > - owlcs/owlapi#863 <owlcs/owlapi#863> > - owlcollab/owltools#286 > <owlcollab/owltools#286> > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#534?email_source=notifications&email_token=AAAMMOIXBHX2WXOT7DYDYW3P7D5AFA5CNFSM4ICSB4G2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G67IEUA>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AAAMMOIUNFNCY46J2WOZOFTP7D5AFANCNFSM4ICSB4GQ> > . >

[althonos]

@cmungall : their OBO is fine, they are using the full IRI of rdfs:seeAlso in a qualifier, which is perfectly valid. The OWL API translation for some reason prefixes it with oboInOwl (which is wrong on the semantic level) and then expands the prefixed ID into a full IRI without percent-escaping (which is wrong on the syntactic level).

I opened an issue on the OWL API issue tracker, but I figured out I would be good to have an issue on ROBOT as well until it is updated to a bugfixed version of the OWL API.