existingOntologyIRI error when loading into Protégé #25
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I don't understand that. The root element has an xml:base defined on line 20, doesn't it? |
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Looks like it's still broken - as is, the ontology cannot be used by any OWL tooling. Let me know if you need help - or if you would like it removed from the OBO Library list of active ontologies (it's causing us problems right now). I expect the problem is that the ontology imports http://www.w3.org/ns/prov# But this isn't an OWL ontology, it's a webpage |
It's both. It's content negotiated. With the correct content type, it returns an OWL ontology: |
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Do we know how the owlapi behaves here?
…On Mon, Apr 24, 2017 at 20:02 Hilmar Lapp ***@***.***> wrote:
But this isn't an OWL ontology, it's a webpage
It's both. It's content negotiated. With the correct content type, it
returns an OWL ontology:
$ curl -sH "Accept: application/rdf+xml" -L http://www.w3.org/ns/prov
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It should work fine. For example, you can load PROV from the URL. That said, it does produce the same errors: |
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BTW the errors also occur if loading the PROV ontology only and directly (using http://www.w3.org/ns/prov-o as URI): |
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FWIW these errors are not fatal in any way in Protégé. It's possible to run a reasoner after loading, for example, without further errors. |
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@stain and/or @paolociccarese do you have any insights here what the problem with PROV-O might be? Perhaps there's a discussion group or forum where this has come up already but I can't find any. Is there an issue tracker that would be applicable? |
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@hlapp well,we started the PROV-O ontology with Protege.. so who to blame? :) I think it has to do with OWL profiles - I'll have a look. Note that importing http://www.w3.org/ns/prov# is wider than just http://www.w3.org/ns/prov-o as the former includes things like inverses and PROV-AQ extensions. |
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I can reproduce with Protege 5.2.0 with both http://www.w3.org/ns/prov-o.ttl and http://www.w3.org/ns/prov-o.rdf The problem seems to be that the PROV ontology uses two of its own object properties as annotation properties to describe the ontology itself. From http://www.w3.org/ns/prov-o.ttl <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> ;
:specializationOf <http://www.w3.org/ns/prov-o> ;
:wasRevisionOf <http://www.w3.org/ns/prov-o-20130312> .
:specializationOf
a owl:AnnotationProperty, owl:ObjectProperty .
# ..
:wasRevisionOf
a owl:AnnotationProperty, owl:ObjectProperty .
# ..This similar mini-ontology causes the same problem: https://gist.github.com/stain/bab50aa1722929c0bc8bb14b9736b874 I could also reproduce it with my OWL profilechecker after updating it for OWLAPI 5.1.0. The PROV ontology RDF/XML file was originally saved with OWLAPI 3.1.0 which didn't complain about this - I see however the warning with OWLAPI 3.4.2 and later. The error message seems to come during loading and does (necessarily) not mean the ontology is invalid according to the profile: However if I don't use the annotation property on the ontology it loads without warning, and the same if I don't declare it explicitly as an AnnotationProperty. As this error is only output to the logger during loading I am not sure how it is causing any problems for miapa (beyond causing worry) - but I'll check with the owlapi gang. |
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I do get a serious error from OWLAPI 5.1 from importing http://www.w3.org/ns/prov# (aka http://www.w3.org/ns/prov.ttl) as it imports http://www.w3.org/ns/prov-o# (aka http://www.w3.org/ns/prov-o.ttl -- however both declare I will flag this with the rest of the PROV folks. (BTW - I don't have problems opening either of them in Protege 5.2.0 - and even https://raw.githubusercontent.com/miapa/miapa/master/ontology/miapa.owl opens fine -- that uses OWLAPI 4) |
The simpler http://www.w3.org/ns/prov-o import (aka http://www.w3.org/ns/prov-o.ttl or http://www.w3.org/ns/prov-o.rdf after content negotation) is preferred to http://www.w3.org/ns/prov#. See also evoinfo#25.
When loading the miapa.owl ontology into Protégé, the following error occurs (once).
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