[Pellet-users] Error in 'compute inferred types' in Protege

Fri Jun 1 02:28:03 UTC 2007

This error looks very similar to a known issue [1] that have been 
already fixed in the SVN. However, this ontology seems to have some 
other problems. There are some cardinality restrictions defined on the 
transitive property has_data_part. Cardinality restrictions on 
transitive properties are not allowed in OWL-DL (because they cause 
undecidabilty) and they are not supported by Pellet. Even if the 
reasoner ignores the transitivity axiom, the ontology turns out to be 
inconsistent. One explanation for the inconsistency is the following set 
of axioms which suggests there is some kind of modeling error:

Type(water_molecule, inorganic_solvent_molecule),
PropertyValue(water_molecule, is_described_by, CAS_7732-18-5),
Type(CAS_7732-18-5, chemical_abstracts_accession_number),
SubClassOf(inorganic_solvent_molecule, solvent_molecule),
SubClassOf(solvent_molecule, all(is_described_by, 
not(substance_accession_number))), 
SubClassOf(chemical_abstracts_accession_number, substance_accession_number)

I haven't checked what would happen if this problem was fixed but I 
believe the exception you get would not happen with the SVN version.

Cheers,
Evren

[1] http://cvsdude.com/trac/clark-parsia/pellet-devel/ticket/3

On 5/30/07 9:49 PM, satya sahoo wrote:
> Hi,
> I am new to using a reasoner. I am using Pellet
> through Protege ontology editor (using command:
> 'pellet-dig.bat -port 2004' and pointing Protege to
> the service). We are working on ProPreO
> ontology(http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/ProPreO.owl)
>
> When I use the OWL -> compute inferred types option, I
> get the following error: 
>
> =======================================================
> java.lang.UnsupportedOperationException
>         at java.util.AbstractList.add(Unknown Source)
>         at java.util.AbstractList.add(Unknown Source)
>         at
> org.mindswap.pellet.taxonomy.TaxonomyNode.addSub(TaxonomyNode.java:18
> 2)
>         at
> org.mindswap.pellet.taxonomy.Taxonomy.mergeNodes(Taxonomy.java:676)
>         at
> org.mindswap.pellet.taxonomy.Taxonomy.merge(Taxonomy.java:577)
>         at
> org.mindswap.pellet.taxonomy.TaxonomyBuilder.addToldEquivalent(Taxono
> myBuilder.java:330)
>         at
> org.mindswap.pellet.taxonomy.TaxonomyBuilder.preclassify(TaxonomyBuil
> der.java:262)
>         at
> org.mindswap.pellet.taxonomy.TaxonomyBuilder.init(TaxonomyBuilder.jav
> a:188)
>         at
> org.mindswap.pellet.taxonomy.TaxonomyBuilder.classify(TaxonomyBuilder
> .java:106)
>         at
> org.mindswap.pellet.KnowledgeBase.classify(KnowledgeBase.java:976)
>         at
> org.mindswap.pellet.KnowledgeBase.realize(KnowledgeBase.java:992)
>         at
> org.mindswap.pellet.KnowledgeBase.getTypes(KnowledgeBase.java:2044)
>         at
> org.mindswap.pellet.dig.DIGAskHandler.types(DIGAskHandler.java:300)
>         at
> org.mindswap.pellet.dig.DIGAskHandler.asks(DIGAskHandler.java:125)
>         at
> org.mindswap.pellet.dig.PelletDIGReasoner.process(PelletDIGReasoner.j
> ava:160)
>         at
> org.mindswap.pellet.dig.PelletDIGReasoner.process(PelletDIGReasoner.j
> ava:112)
>         at
> org.mindswap.pellet.dig.PelletDIGReasoner.process(PelletDIGReasoner.j
> ava:102)
>         at
> org.mindswap.pellet.dig.PelletDIGServer.handle(PelletDIGServer.java:7
> 4)
>         at
> org.mortbay.http.HttpContext.handle(HttpContext.java:1565)
>         at
> org.mortbay.http.HttpContext.handle(HttpContext.java:1517)
>         at
> org.mortbay.http.HttpServer.service(HttpServer.java:954)
>         at
> org.mortbay.http.HttpConnection.service(HttpConnection.java:816)
>         at
> org.mortbay.http.HttpConnection.handleNext(HttpConnection.java:983)
>         at
> org.mortbay.http.HttpConnection.handle(HttpConnection.java:833)
>         at
> org.mortbay.http.SocketListener.handleConnection(SocketListener.java:
> 244)
>         at
> org.mortbay.util.ThreadedServer.handle(ThreadedServer.java:357)
>         at
> org.mortbay.util.ThreadPool$PoolThread.run(ThreadPool.java:534)
> DEBUG [SocketListener0-0] (PelletDIGReasoner.java:126)
> -
> <?xml version="1.0" encoding="UTF-8"?>
> <response xmlns="http://dl.kr.org/dig/2003/02/lang"
> xmlns:xsi="http://www.w3.org
> /2001/XMLSchema-instance"
> xsi:schemaLocation="http://dl.kr.org/dig/2003/02/lang
>      http://dl-web.man.ac.uk/dig/2003/02/dig.xsd">
>     <error code="400" message="General Ask Error"/>
> </response>
>
>
> DEBUG [SocketListener0-0] (PelletDIGReasoner.java:110)
> -
> <?xml version="1.0" encoding="UTF-8"?>
> <releaseKB
> uri="urn:dig:pellet:kb3d9fa169:112df628ac8:-7ffc"
> xmlns="http://dl.kr
> .org/dig/2003/02/lang"/>
>
>
> DEBUG [SocketListener0-0] (PelletDIGReasoner.java:126)
> -
> <?xml version="1.0" encoding="UTF-8"?>
> <response xmlns="http://dl.kr.org/dig/2003/02/lang"
> xmlns:xsi="http://www.w3.org
> /2001/XMLSchema-instance"
> xsi:schemaLocation="http://dl.kr.org/dig/2003/02/lang
>      http://dl-web.man.ac.uk/dig/2003/02/dig.xsd">
>     <ok/>
> </response>
> =======================================================
>
>
> Any suggestions regarding this error would be greatly
> appreciated.
>
> Thanks.
>
> Satya
>
>
>
>        
> ____________________________________________________________________________________Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out.
> http://answers.yahoo.com/dir/?link=list&sid=396545469
> _______________________________________________
> Pellet-users mailing list
> Pellet-users at lists.owldl.com
> http://lists.owldl.com/mailman/listinfo/pellet-users
> _______________________________________________
>
> Sponsored by Clark & Parsia, LLC http://clarkparsia.com/
>   