Re: Illegal punning in prov-o.ttl, prov.ttl imports broken

Hi Stian,

Can we break these down into the specific changes you want, namely, the
removal of

   :wasRevisionOf  a owl:AnnotationProperty, ;
  :specializationOf  a owl:AnnotationProperty,

These will have to be done in an errata? I believe we can update the
ontologies directly but need to see what Ivan suggests here.

Thanks for catching this,
Paul



On Thu, May 4, 2017 at 5:33 PM, Stian Soiland-Reyes <
soiland-reyes@manchester.ac.uk> wrote:

> Hi, hope you are all well!
>
> It was raised to my attention [1] that our http://www.w3.org/ns/prov-o
> (aka https://www.w3.org/ns/prov-o.ttl or
> https://www.w3.org/ns/prov-o.rdf) has an illegal OWL 2 punning of an
> annotation property and object property, and that this causes error
> messages (but no apparant issues) when loading the ontology in Protege -
> reported by the underlying OWLAPI.
>
> Using my updated OWL2 ProfileChecker 1.1.0 [2] (which uses OWLAPI 5.1):
>
>     stain@biggiebuntu:~$ profilechecker http://www.w3.org/ns/prov-o --all
>     [main] ERROR uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl -
>     Illegal redeclarations of entities: reuse of entity
>     http://www.w3.org/ns/prov#wasRevisionOf in punning not allowed
>     [Declaration(ObjectProperty(<http://www.w3.org/ns/prov#wasRevisionOf
> >)),
>     Declaration(AnnotationProperty(<http://www.w3.org/ns/prov#
> wasRevisionOf>))]
>     [main] ERROR uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl -
>     Illegal redeclarations of entities: reuse of entity
>     http://www.w3.org/ns/prov#specializationOf in punning not allowed
>     [Declaration(ObjectProperty(<http://www.w3.org/ns/prov#
> specializationOf>)),
>     Declaration(AnnotationProperty(<http://www.w3.org/ns/prov#
> specializationOf>))]
>
>     OWL2_DL: 9 violations
>     OWL2_QL: 29 violations
>     OWL2_EL: 32 violations
>     OWL2_RL: 16 violations
>     OWL2_FULL: 9 violations
>
> See gist [3] for all the OWL2 Full violations.
>
>
> This seems to be because our prov-o.ttl (and .rdf) declares
> prov:wasRevisionOf and prov:specializationOf as both ObjectProperty and
> AnnotationProperty.
>
>
>     :wasRevisionOf
>         a owl:AnnotationProperty, owl:ObjectProperty ;
>
>
>     :specializationOf
>         a owl:AnnotationProperty, owl:ObjectProperty ;
>
> While this punning is allowed for OWL2 Full - it is
> not allowed in RDF serializations of OWL ontologies [4]
> because an IRI or BlankNode must be assigned  to "at most one" of object
> property expressions, data property expression or annotation property.
>
>
> I think we did the above because we also declare provenance of the
> owl:Ontology within the same file:
>
>
>   <http://www.w3.org/ns/prov-o#>
>     a owl:Ontology ;
>     rdfs:label "W3C PROVenance Interchange Ontology (PROV-O)"@en ;
>     rdfs:seeAlso <http://www.w3.org/TR/prov-o/>, <
> http://www.w3.org/ns/prov> ;
>     owl:versionIRI <http://www.w3.org/ns/prov-o-20130430> ;
>     owl:versionInfo "Recommendation version 2013-04-30"@en ;
>     :specializationOf <http://www.w3.org/ns/prov-o> ;
>     :wasRevisionOf <http://www.w3.org/ns/prov-o-20120312> .
>
> Ironically the AnnotationProperty declaration is something Protege/OWLAPI
> added
> automatically at the time because of this - and in fact if "a
> owl:AnnotationProperty" is not implicitly declared (but it is still stated
> on
> the owl:Ontology), then there is no warning at all from OWLAPI:
>
>     stain@biggiebuntu:~/Desktop$ profilechecker prov-o.ttl --all
>     OWL2_DL: OK
>     OWL2_QL: 20 violations
>     OWL2_EL: 23 violations
>     OWL2_RL: 7 violations
>     OWL2_FULL: OK
>
> Note how the above now is OWL2 DL compliant again.  I double-checked the
> history - and when we did profile checking the OWLAPI didn't do this
> punning check - it was introduced just a few months after our release.
>
>
> So I would suggest that we fix prov-o.ttl and prov-o.rdf to remove the
> explicit
> AnnotationProperty statement.  If you agree we can also remove it from the
> statements on the owl:Ontology itself (that is anyway covered by the
> provenance
> file) - although for Protege/OWLAPI that doesn't seem necessary.
>
> ----
>
> There's a larger issue, in that the "all in one go"
> http://www.w3.org/ns/prov (aka https://www.w3.org/ns/prov.ttl) declares:
>
>
>     <http://www.w3.org/ns/prov#>
>         a owl:Ontology ;
>
> and also https://www.w3.org/ns/prov-o.ttl declares:
>
>
>     <http://www.w3.org/ns/prov#>
>         a owl:Ontology .
>
> This causes loading exceptions in OWLAPI 5 [6], including:
>
>     Exception in thread "main" org.semanticweb.owlapi.model.UnloadableImportException:
> Could not load imported ontology: <http://www.w3.org/ns/prov-aq#> Cause:
> Ontology already exists. OntologyID(OntologyIRI(<http:/
> /www.w3.org/ns/prov#>) VersionIRI(<null>))
>
>
> This prevents http://www.w3.org/ns/prov being used as "owl:imports" in
> other ontologies.
>
>
> Given that we use "/ns/prov-o#" as name in:
>
>     rdfs:isDefinedBy <http://www.w3.org/ns/prov-o#> ;
>
> then I think this should be the owl:Ontology IRI within prov-o.ttl and
> friends - that is the style we've used say in
> http://www.w3.org/ns/prov-o-inverses
> and would prevent conflict with prov.ttl.
>
>
>
> I also wonder why prov.ttl both does an owl:imports AND re-declares all the
> concepts (and multiple owl:Ontology), which seems a bit pointless, as well
> as
> causing their owl:Ontology to be declared both within prov.ttl and
> prov-o.ttl
> -- perhaps that also gives errors.  Suggested fix is for prov.ttl and
> friends
> to only have the imports - or at least to not have repeated owl:Ontology
> declarations.
>
>
>
> [1] https://github.com/evoinfo/miapa/issues/25
> [2] https://github.com/stain/profilechecker/releases/tag/1.1.0
> [3] https://gist.github.com/stain/1c61313ab1b5349d3cba6467c7c51a2d
> [4] https://sourceforge.net/p/owlapi/mailman/message/31757311/
> [5] https://www.w3.org/TR/owl2-mapping-to-rdf/#Populating_an_Ontology
> [6] https://gist.github.com/stain/9f1c5caeb32b618547ca63612edfd6e7
>
>
> --
> Stian Soiland-Reyes
> The University of Manchester
> http://www.esciencelab.org.uk/
> http://orcid.org/0000-0001-9842-9718
>
>
>