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Re: [p4-feedback] [Pellet-users] Protege4 & Pellet compatibility

From: Rinke Hoekstra <hoekstra@uva.nl>
Date: Fri, 16 May 2008 13:15:15 +0200
Cc: pellet-users@lists.owldl.com, OWL Working Group WG <public-owl-wg@w3.org>
Message-Id: <7D0A8AF1-3F14-4A9E-BD3E-90D86E8A26B2@uva.nl>
To: "Submit feedback for Protege 4.0 alpha" <p4-feedback@mailman.stanford.edu>

CC to the OWL WG

Hi Matthew,

I remember an issue about this (ISSUE-106) on the OWL working group.  
We actually decided that all OWL2 vocabulary should go into the old  
OWL namespace. See the minutes at [1], and the issue description here  
[2] (btw. there's a typo in the minutes saying that this resolves  
ISSUE 57, but it really should be ISSUE 106)

NB: this does not hold for the new OWL XML syntax namespace..

Best,

	Rinke

[1] http://www.w3.org/2007/OWL/wiki/Teleconference.2008.04.23/Minutes
[2] http://www.w3.org/2007/OWL/tracker/issues/106



On 16 mei 2008, at 12:59, Matthew Horridge wrote:

> Unfortunately this does look like a version issue.  It seems that
> Protege 4 uses an updated version of the OWL API and Pellet uses a
> previous version.  The problem is really due to the changing of the
> namespace for OWL 2 which was accommodated in the latest OWL API.
>
> Also, you should also note that you can't use the wonderweb validator
> to validate ontologies that contain OWL 2 constructs (such as
> qualified cardinality restrictions).
>
> Cheers,
>
> Matthew
>
>
> On 16 May 2008, at 11:10, Nick Drummond wrote:
>
>> Yes, I've verified this. The OWLAPI version is not the issue.
>>
>> I think this is pellet's loader that is misinterpreting the
>> owl2:onClass statement in the qualified cardinality restrictions.
>>
>> I had a look at the code and the vocabulary is using the owl11
>> namespace for onClass. Switching this gets the first part of the
>> issue resolved but I am still getting the following:
>>
>> Non OWL-DL features used:
>> Multiple Types: Resource owl11:onClass  is used as an individual but
>> defined as aclass
>> Untyped Individual: Assuming restriction(intersection-test:p1
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming intersection-test:intersect is an
>> individual
>> Untyped Individual: Assuming restriction(intersection-test:p1
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p2
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p4
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p3
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p3
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming intersection-test:multiple_eq is an
>> individual
>> Untyped Individual: Assuming restriction(intersection-test:p2
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p4
>> minCardinality(2)) is an individual
>> Untyped Property: Assuming intersection-test:p1 is an object property
>> Untyped Property: Assuming owl11:onClass is an object property
>> Untyped Property: Assuming intersection-test:p3 is an object property
>> Untyped Property: Assuming intersection-test:p4 is an object property
>> Untyped Property: Assuming intersection-test:p2 is an object property
>> Non OWL-Lite features used:
>> Anonymous Intersection Class: owl:intersectionOf triples cannot have
>> an anonymous subject in OWL Lite
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p1 minCardinality(2))
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p2 minCardinality(2))
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p3 minCardinality(2))
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p4 minCardinality(2))
>>
>> Add the following statements to make this document OWL DL
>> <rdf:RDF
>>    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>    xmlns:owl="http://www.w3.org/2002/07/owl#" >
>>  <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#p2
>> ">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty
>> "/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#intersect
>> ">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p3,1,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p1,1,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p1,2,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#p4
>> ">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty
>> "/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#p1
>> ">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty
>> "/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p2,1,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p2,2,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="http://www.w3.org/2006/12/
>> owl11#onClass">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty
>> "/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p3,2,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p4,2,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p4,1,( 
>> )
>> )">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#multiple_eq
>> ">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>>  </rdf:Description>
>>  <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#p3
>> ">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty
>> "/>
>>  </rdf:Description>
>> </rdf:RDF>
>>
>>
>> On Fri, May 16, 2008 at 9:18 AM, Rinke Hoekstra <hoekstra@uva.nl>
>> wrote:
>> Hi,
>>
>> I've noticed recently that Pellet 1.5.2 does not swallow the RDF/OWL
>> files produced by Protege 4. Although everything seems to work fine
>> in P4 (build 62) for the attached ontology (which I built to test
>> some other possible bug/problem I will report on later), pellet
>> complains with the trace below.
>>
>> I guess it has something to do with the different ways in which
>> Pellet and Protege deal with OWL2 constructs (do they use a
>> different version of the OWLAPI?)
>>
>> -Rinke
>>
>>
>>
>>
>>
>> Input file: file:/Users/hoekstra/Projects/ontologies/thesis-studies/
>> intersection-test.owl
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7ffa @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fe1 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fec @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fe3 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fe4 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7ff3 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fe5 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fe6 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7ff5 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7ff8 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fea @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> WARN [main] (OWLLoader.java:364) - Unsupported axiom: Ignoring
>> class expression used in subject position:
>> 2b6188b8:119f0cbf5f8:-7fe0 @http://www.w3.org/2006/12/owl2#onClass http://www.leibnizcenter.org/ontostore/intersection-test.owl#Dummy
>> OWL Species: Full
>> DL Expressivity: ALCF
>> Consistent: Yes
>> Time: 1975 ms (Loading: 1444 Species Validation: 139 Consistency:
>> 151 Classification: 54 Realization: 186 )
>>
>> Classification:
>>
>> owl:Thing - (intersection-test:dummy2)
>>   intersection-test:Dummy - (intersection-test:dummy)
>>   intersection-test:Intersection_cardinality
>>      intersection-test:Intersection - (intersection-test:intersect)
>>         intersection-
>> test:Intersection_multiple_cardinality_someValuesFrom
>>      intersection-test:Intersection_multiple_cardinality
>>         intersection-
>> test:Intersection_multiple_cardinality_someValuesFrom
>>   intersection-test:MultipleEquivalences_cardinality
>>      intersection-test:MultipleEquivalences = intersection-
>> test:MultipleEquivalences_multiple_cardinality = intersection-
>> test:MultipleEquivalences_multiple_cardinality_someValuesFrom -
>> (intersection-test:multiple_eq)
>>
>>
>> Non OWL-DL features used:
>> Multiple Types: Resource owl2:onClass  is used as an individual but
>> defined as aclass
>> Untyped Individual: Assuming restriction(intersection-test:p1
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p2
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p4
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p3
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p3
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming intersection-test:multiple_eq is an
>> individual
>> Untyped Individual: Assuming restriction(intersection-test:p2
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p4
>> minCardinality(2)) is an individual
>> Untyped Individual: Assuming restriction(intersection-test:p1
>> minCardinality(1)) is an individual
>> Untyped Individual: Assuming intersection-test:intersect is an
>> individual
>> Untyped Individual: Assuming intersection-test:dummy2 is an  
>> individual
>> Untyped Property: Assuming owl2:onClass is an object property
>> Non OWL-Lite features used:
>> Anonymous Intersection Class: owl:intersectionOf triples cannot have
>> an anonymous subject in OWL Lite
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p1 minCardinality(2))
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p2 minCardinality(2))
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p3 minCardinality(2))
>> Cardinality Restriction: minCardinality value is greater than 1
>> restriction(intersection-test:p4 minCardinality(2))
>>
>> Add the following statements to make this document OWL DL
>> <rdf:RDF
>>   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>   xmlns:owl="http://www.w3.org/2002/07/owl#" >
>> <rdf:Description rdf:about="http://www.w3.org/2006/12/owl2#onClass">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/ 
>> owl#ObjectProperty
>> "/>
>> </rdf:Description>
>> <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#dummy2
>> ">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#intersect
>> ">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p3,1,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p1,1,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p1,2,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p2,1,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p4,2,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p4,1,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p2,2,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="min(http://www.leibnizcenter.org/ontostore/intersection-test.owl#p3,2,( 
>> )
>> )">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> <rdf:Description rdf:about="http://www.leibnizcenter.org/ontostore/intersection-test.owl#multiple_eq
>> ">
>>   <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
>> </rdf:Description>
>> </rdf:RDF>
>>
>>
>> -----------------------------------------------
>> Drs. Rinke Hoekstra
>>
>> Email: hoekstra@uva.nl    Skype:  rinkehoekstra
>> Phone: +31-20-5253499     Fax:   +31-20-5253495
>> Web:   http://www.leibnizcenter.org/users/rinke
>>
>> Leibniz Center for Law,          Faculty of Law
>> University of Amsterdam,            PO Box 1030
>> 1000 BA  Amsterdam,             The Netherlands
>> -----------------------------------------------
>>
>>
>>
>>
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-----------------------------------------------
Drs. Rinke Hoekstra

Email: hoekstra@uva.nl    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------
Received on Friday, 16 May 2008 11:16:00 GMT

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