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Reasoning Error using Reasoner Tab

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Reasoning Error using Reasoner Tab

Ullah, Izhar
Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 

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Re: Reasoning Error using Reasoner Tab

Rafael Gonçalves
Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Reasoning Error using Reasoner Tab

Ullah, Izhar
Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Reasoning Error using Reasoner Tab

Rafael Gonçalves
Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Reasoning Error using Reasoner Tab

Ullah, Izhar
Hi Rafael,

I really appreciate your help. It makes sense. Could you please give me one more favour by marking those malformed XML literals in my ontology file and send it at my gmail address? I will be grateful.

Many thanks once again.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 21:24
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Reasoning Error using Reasoner Tab

Rafael Gonçalves
Hi Izhar,

You’re welcome. I didn’t produce a list unfortunately, as there are a lot of occurrences.  What I did was go to the ‘Datatypes' view in the ‘Entities' tab, select the 'rdf:XMLLiteral' datatype, and then on the right side click on the 'Datatype Usage’ view. You’ll see a list of axioms where that datatype is used. Some of them use the datatype correctly, others not—it should be easy to spot the ones that don’t start with an XML tag.

Cheers,
Rafael

On May 16, 2017, at 13:54, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I really appreciate your help. It makes sense. Could you please give me one more favour by marking those malformed XML literals in my ontology file and send it at my gmail address? I will be grateful.

Many thanks once again.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 21:24
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Reasoning Error using Reasoner Tab

Ullah, Izhar
Oh I see, these are the literals from the imported ontology MUO/UCUM for measuring units.
I owe you a great debt of gratitude for your time, help and valuable suggestions.

Best,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 23:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

You’re welcome. I didn’t produce a list unfortunately, as there are a lot of occurrences.  What I did was go to the ‘Datatypes' view in the ‘Entities' tab, select the 'rdf:XMLLiteral' datatype, and then on the right side click on the 'Datatype Usage’ view. You’ll see a list of axioms where that datatype is used. Some of them use the datatype correctly, others not—it should be easy to spot the ones that don’t start with an XML tag.

Cheers,
Rafael

On May 16, 2017, at 13:54, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I really appreciate your help. It makes sense. Could you please give me one more favour by marking those malformed XML literals in my ontology file and send it at my gmail address? I will be grateful.

Many thanks once again.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 21:24
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
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https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Reasoning Error using Reasoner Tab

Ullah, Izhar
In reply to this post by Rafael Gonçalves
Hi Rafael,

I corrected/modified all those malformed xmlLiterals and then ran the reasoner (Hermit 1.3.8). Though I didn't get those errors regarding malformed literals, however, now it says the ontology is inconsistent. I deleted all the instances from the ontology and ran the reasoner again but still, a lot of classes have been shown red which, if I'm not wrong, means inconsistent. Could you please have a look at my ontology file and see why these classes are inconsistent? Your help would be really appreciated.

PS. I have sent you my ontology file on your email address both with instances and without instances. 

If you need further information please let me know.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 23:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

You’re welcome. I didn’t produce a list unfortunately, as there are a lot of occurrences.  What I did was go to the ‘Datatypes' view in the ‘Entities' tab, select the 'rdf:XMLLiteral' datatype, and then on the right side click on the 'Datatype Usage’ view. You’ll see a list of axioms where that datatype is used. Some of them use the datatype correctly, others not—it should be easy to spot the ones that don’t start with an XML tag.

Cheers,
Rafael

On May 16, 2017, at 13:54, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I really appreciate your help. It makes sense. Could you please give me one more favour by marking those malformed XML literals in my ontology file and send it at my gmail address? I will be grateful.

Many thanks once again.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 21:24
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Reasoning Error using Reasoner Tab

samsontu
Had you tried Protege's “explanation” feature to understand why your ontology is inconsistent? Click on the “?” icon to the right of Nothing, as shown in the screen dump below.

It’s better to figure out something yourself.

With best regards,
Samson



Image result for protege explanation
On May 25, 2017, at 12:04 PM, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I corrected/modified all those malformed xmlLiterals and then ran the reasoner (Hermit 1.3.8). Though I didn't get those errors regarding malformed literals, however, now it says the ontology is inconsistent. I deleted all the instances from the ontology and ran the reasoner again but still, a lot of classes have been shown red which, if I'm not wrong, means inconsistent. Could you please have a look at my ontology file and see why these classes are inconsistent? Your help would be really appreciated.

PS. I have sent you my ontology file on your email address both with instances and without instances. 

If you need further information please let me know.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 23:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

You’re welcome. I didn’t produce a list unfortunately, as there are a lot of occurrences.  What I did was go to the ‘Datatypes' view in the ‘Entities' tab, select the 'rdf:XMLLiteral' datatype, and then on the right side click on the 'Datatype Usage’ view. You’ll see a list of axioms where that datatype is used. Some of them use the datatype correctly, others not—it should be easy to spot the ones that don’t start with an XML tag.

Cheers,
Rafael

On May 16, 2017, at 13:54, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I really appreciate your help. It makes sense. Could you please give me one more favour by marking those malformed XML literals in my ontology file and send it at my gmail address? I will be grateful.

Many thanks once again.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 21:24
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
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Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944




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Re: Reasoning Error using Reasoner Tab

Ullah, Izhar
Hi Samson,

I haven't tried the explanation feature yet and that seems very useful. I'll definitely do.

Many thanks,

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Samson Tu [[hidden email]]
Sent: 25 May 2017 20:25
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Had you tried Protege's “explanation” feature to understand why your ontology is inconsistent? Click on the “?” icon to the right of Nothing, as shown in the screen dump below.

It’s better to figure out something yourself.

With best regards,
Samson



Image result for protege explanation
On May 25, 2017, at 12:04 PM, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I corrected/modified all those malformed xmlLiterals and then ran the reasoner (Hermit 1.3.8). Though I didn't get those errors regarding malformed literals, however, now it says the ontology is inconsistent. I deleted all the instances from the ontology and ran the reasoner again but still, a lot of classes have been shown red which, if I'm not wrong, means inconsistent. Could you please have a look at my ontology file and see why these classes are inconsistent? Your help would be really appreciated.

PS. I have sent you my ontology file on your email address both with instances and without instances. 

If you need further information please let me know.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 23:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

You’re welcome. I didn’t produce a list unfortunately, as there are a lot of occurrences.  What I did was go to the ‘Datatypes' view in the ‘Entities' tab, select the 'rdf:XMLLiteral' datatype, and then on the right side click on the 'Datatype Usage’ view. You’ll see a list of axioms where that datatype is used. Some of them use the datatype correctly, others not—it should be easy to spot the ones that don’t start with an XML tag.

Cheers,
Rafael

On May 16, 2017, at 13:54, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

I really appreciate your help. It makes sense. Could you please give me one more favour by marking those malformed XML literals in my ontology file and send it at my gmail address? I will be grateful.

Many thanks once again.

Best,

Izhar

From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 21:24
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

Thanks for sending the ontology. I noticed that there are multiple malformed XML literals in the ontology. The values of these literals should be valid, self-contained XML. In the ontology there are occurrences of literals such as “some <tag>content</tag>”, which should be fixed into “<tag>some content</tag>.

That said, the error you encountered seems related to the reasoner. I opened an issue in a GitHub fork of Hermit: https://github.com/phillord/hermit-reasoner/issues/7.

Regarding the FaCT++ issue. I reasoned over the ontology in Protege 5.2, and there are uses of datatypes that are not supported in OWL 2, such as gMonth, gDay, etc. The allowed datatypes in OWL 2 are listed at: https://www.w3.org/TR/owl2-syntax/#Datatype_Maps.

Hope this helps.

Cheers,
Rafael

On May 16, 2017, at 12:15, Ullah, Izhar <[hidden email]> wrote:

Hi Rafael,

Thanks for your reply. Certainly I do, I will send it to you at your email address. Just a humble request please don't disclose the ontology and keep it at a secure place because the ontology is highly confidential so I would be grateful if you could not disclose/share my ontology to/with anyone else.

By the way, when I used the FaCT++ reasoner in Protege 4.1, I got the following error:

Error 1 Logged at Tue May 16 20:04:58 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)
---------------------------------------------------------------------------------------------------

Error 2 Logged at Tue May 16 20:05:13 BST 2017
OWLRuntimeException: Not a built in datatype.  The getBuiltInDatatype() method should only be called on built in datatypes.
    uk.ac.manchester.cs.owl.owlapi.OWLDatatypeImpl.getBuiltInDatatype(OWLDatatypeImpl.java:164)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.toDataValuePointer(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner$AxiomTranslator.visit(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:102)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadAxiom(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.loadReasonerAxioms(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner.<init>(Unknown Source)
    uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory.createReasoner(Unknown Source)
    org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:343)
    org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:315)
    java.lang.Thread.run(Thread.java:695)

Best regards,

Izhar


From: protege-user [[hidden email]] on behalf of Rafael Gonçalves [[hidden email]]
Sent: 16 May 2017 19:12
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Reasoning Error using Reasoner Tab

Hi Izhar,

This looks like a dependency issue with the HermiT reasoner. Could you please provide the ontology (or a subset of it) that we can reproduce this issue with?

Cheers,
Rafael

On May 16, 2017, at 06:52, Ullah, Izhar <[hidden email]> wrote:

Hi all,

I am using Protege 5.2 and want to reason over my ontology. I selected Reasoner ->Hermit 1.3.8 and started the reasoning process but got the following error:

2017-05-16 14:38:09.680 [Classification Thread] INFO  OWLReasonerManager    
2017-05-16 14:38:09.694 [Classification Thread] ERROR OWLReasonerManager    An error occurred during reasoning: javax/xml/stream/XMLStreamException.
java.lang.NoClassDefFoundError: javax/xml/stream/XMLStreamException
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteral.parse(XMLLiteral.java:33) ~[na:na]
at org.semanticweb.HermiT.datatypes.xmlliteral.XMLLiteralDatatypeHandler.parseLiteral(XMLLiteralDatatypeHandler.java:45) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:199) ~[na:na]
at org.semanticweb.HermiT.Reasoner.<init>(Reasoner.java:173) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createHermiTOWLReasoner(ReasonerFactory.java:51) ~[na:na]
at org.semanticweb.HermiT.ReasonerFactory.createReasoner(ReasonerFactory.java:19) ~[na:na]
at org.protege.editor.owl.model.inference.ReasonerUtilities.createReasoner(ReasonerUtilities.java:20) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:428) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:386) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: java.lang.ClassNotFoundException: javax.xml.stream.XMLStreamException not found by org.semanticweb.hermit [27]
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77) ~[org.apache.felix.main.jar:na]
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993) ~[org.apache.felix.main.jar:na]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_40]
... 19 common frames omitted
 

Can someone please help me out to resolve the issue?

If you require any further information please let me know.

Many thanks in advance.

Best,

Izhar,
Doctoral Scholar,
Lancaster University, UK 
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944



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