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Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools
http://www.evoio.org/wiki/MIAPA
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existingOntologyIRI error when loading into Protégé #25

Open hlapp opened 7 years ago

hlapp commented 7 years ago

When loading the miapa.owl ontology into Protégé, the following error occurs (once).

Level:       INFO
Time:        1478717592498
Message:     Notice: root element does not have an xml:base. Relative IRIs will be resolved against http://www.w3.org/ns/prov-aq#

Level:       ERROR
Time:        1478717592500
Message:     OWLOntologyManagerImpl.checkForOntologyIDChange() existing:Ontology(OntologyID(OntologyIRI(<http://www.w3.org/ns/prov#>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0] First 20 axioms: {}

Level:       ERROR
Time:        1478717592501
Message:     OWLOntologyManagerImpl.checkForOntologyIDChange() new:Ontology(OntologyID(Anonymous-14)) [Axioms: 7 Logical Axioms: 0] First 20 axioms: {Declaration(ObjectProperty(owl:topObjectProperty)) Declaration(AnnotationProperty(rdfs:isDefinedBy)) Declaration(AnnotationProperty(rdfs:label)) Declaration(Class(owl:Thing)) Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(owl:versionInfo)) }
arlin commented 7 years ago

I don't understand that. The root element has an xml:base defined on line 20, doesn't it?

cmungall commented 7 years ago

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

hlapp commented 7 years ago

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
cmungall commented 7 years ago

Do we know how the owlapi behaves here? On Mon, Apr 24, 2017 at 20:02 Hilmar Lapp notifications@github.com 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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hlapp commented 7 years ago

Do we know how the owlapi behaves here?

It should work fine. For example, you can load PROV from the URL. That said, it does produce the same errors:

Level:       INFO
Time:        1493128365595
Message:     ------------------------------- Loading Ontology -------------------------------

Level:       INFO
Time:        1493128365595
Message:     Loading ontology from http://www.w3.org/ns/prov#

Level:       INFO
Time:        1493128365773
Message:     Notice: root element does not have an xml:base. Relative IRIs will be resolved against http://www.w3.org/ns/prov#

Level:       INFO
Time:        1493128365780
Message:     Imported ontology document http://www.w3.org/ns/prov-o# was not resolved to any documents defined in the ontology catalog.

Level:       ERROR
Time:        1493128366039
Message:     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>))]

Level:       ERROR
Time:        1493128366042
Message:     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>))]

Level:       INFO
Time:        1493128366044
Message:     Finished loading imported ontology at http://www.w3.org/ns/prov-o#

Level:       INFO
Time:        1493128366046
Message:     Imported ontology document http://www.w3.org/ns/prov-o-inverses# was not resolved to any documents defined in the ontology catalog.

Level:       INFO
Time:        1493128366122
Message:     Notice: root element does not have an xml:base. Relative IRIs will be resolved against http://www.w3.org/ns/prov-o-inverses#

Level:       ERROR
Time:        1493128366136
Message:     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>))]

Level:       ERROR
Time:        1493128366137
Message:     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>))]

Level:       INFO
Time:        1493128366137
Message:     Finished loading imported ontology at http://www.w3.org/ns/prov-o-inverses#

Level:       INFO
Time:        1493128366138
Message:     Imported ontology document http://www.w3.org/ns/prov-aq# was not resolved to any documents defined in the ontology catalog.

Level:       INFO
Time:        1493128366207
Message:     Notice: root element does not have an xml:base. Relative IRIs will be resolved against http://www.w3.org/ns/prov-aq#

Level:       ERROR
Time:        1493128366208
Message:     OWLOntologyManagerImpl.checkForOntologyIDChange() existing:Ontology(OntologyID(OntologyIRI(<http://www.w3.org/ns/prov#>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0] First 20 axioms: {}

Level:       ERROR
Time:        1493128366209
Message:     OWLOntologyManagerImpl.checkForOntologyIDChange() new:Ontology(OntologyID(Anonymous-8)) [Axioms: 7 Logical Axioms: 0] First 20 axioms: {Declaration(ObjectProperty(owl:topObjectProperty)) Declaration(AnnotationProperty(rdfs:isDefinedBy)) Declaration(AnnotationProperty(rdfs:label)) Declaration(Class(owl:Thing)) Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(owl:versionInfo)) }

Level:       INFO
Time:        1493128366210
Message:     Failed to load imported ontology at http://www.w3.org/ns/prov-aq#

Level:       INFO
Time:        1493128366211
Message:     Imported ontology document http://www.w3.org/ns/prov-dc# was not resolved to any documents defined in the ontology catalog.

Level:       INFO
Time:        1493128366279
Message:     Notice: root element does not have an xml:base. Relative IRIs will be resolved against http://www.w3.org/ns/prov-dc#

Level:       ERROR
Time:        1493128366284
Message:     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>))]

Level:       ERROR
Time:        1493128366285
Message:     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>))]

Level:       INFO
Time:        1493128366285
Message:     Finished loading imported ontology at http://www.w3.org/ns/prov-dc#

Level:       INFO
Time:        1493128366286
Message:     Imported ontology document http://www.w3.org/ns/prov-dictionary# was not resolved to any documents defined in the ontology catalog.

Level:       INFO
Time:        1493128366392
Message:     Finished loading imported ontology at http://www.w3.org/ns/prov-dictionary#

Level:       INFO
Time:        1493128366393
Message:     Imported ontology document http://www.w3.org/ns/prov-links# was not resolved to any documents defined in the ontology catalog.

Level:       INFO
Time:        1493128366465
Message:     Notice: root element does not have an xml:base. Relative IRIs will be resolved against http://www.w3.org/ns/prov-links#

Level:       ERROR
Time:        1493128366469
Message:     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>))]

Level:       ERROR
Time:        1493128366469
Message:     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>))]

Level:       INFO
Time:        1493128366469
Message:     Finished loading imported ontology at http://www.w3.org/ns/prov-links#

Level:       ERROR
Time:        1493128366528
Message:     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>))]

Level:       ERROR
Time:        1493128366528
Message:     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>))]

Level:       INFO
Time:        1493128366529
Message:     Finished loading http://www.w3.org/ns/prov#

Level:       INFO
Time:        1493128366561
Message:     Loading for ontology and imports closure successfully completed in 965 ms
hlapp commented 7 years ago

BTW the errors also occur if loading the PROV ontology only and directly (using http://www.w3.org/ns/prov-o as URI):

Level:       INFO
Time:        1493128788653
Message:     OWL API Version: 4.2.6.20160910-2108

Level:       INFO
Time:        1493128788686
Message:     Loading default configuration parameters for class org.semanticweb.elk.reasoner.config.ReasonerConfiguration

Level:       INFO
Time:        1493128788707
Message:     ------------------------------- Loading Ontology -------------------------------

Level:       INFO
Time:        1493128788707
Message:     Loading ontology from http://www.w3.org/ns/prov-o

Level:       ERROR
Time:        1493128790566
Message:     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>))]

Level:       ERROR
Time:        1493128790569
Message:     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>))]

Level:       INFO
Time:        1493128790571
Message:     Finished loading http://www.w3.org/ns/prov-o

Level:       INFO
Time:        1493128790591
Message:     Loading for ontology and imports closure successfully completed in 1884 ms
hlapp commented 7 years ago

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.

hlapp commented 7 years ago

@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?

stain commented 7 years ago

@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.

stain commented 7 years ago

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

OWL API Version: 4.2.8.20170104-2310 
Loading default configuration parameters for class org.semanticweb.elk.reasoner.config.ReasonerConfiguration 
------------------------------- Loading Ontology ------------------------------- 
Loading ontology from http://www.w3.org/ns/prov-o 
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>))] 
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>))]

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:

stain@biggiebuntu:~$ profilechecker https://gist.githubusercontent.com/stain/bab50aa1722929c0bc8bb14b9736b874/raw/b7b212b0e27e6d0b4e2fa0f3ff9d3fabc79fdb99/punnedAnnotation.ttl Full
[main] ERROR uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl - Illegal redeclarations of entities: reuse of entity http://example.com/annotatedOntology#property1 in punning not allowed [Declaration(AnnotationProperty(<http://example.com/annotatedOntology#property1>)), Declaration(ObjectProperty(<http://example.com/annotatedOntology#property1>))]
Cannot pun between properties: <http://example.com/annotatedOntology#property1> [ObjectPropertyAssertion(<http://example.com/annotatedOntology#property1> <http://example.com/annotatedOntology#> <http://example.com/other>) in OntologyID(OntologyIRI(<http://example.com/annotatedOntology#>) VersionIRI(<http://example.com/annotatedOntology/0.1.0>))]

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.

stain commented 7 years ago

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 <http://www.w3.org/ns/prov#> as ontology, which OWLAPI 5 is not very happy about.

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)

stain commented 7 years ago

Also reported to prov-comments