error in opening ontology

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error in opening ontology

Tanumeet Kaur Juneja
Hi 
I am trying to open an ontology available at the link


in protege 4.1 and getting the following list of errors..could any1 pls tell what could be the possible reason for these errors...
Thanks a lot.












Error 1 Logged at Sun Nov 27 19:36:25 IST 2011
RuntimeException: java.lang.RuntimeException: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: <http://soft.vub.ac.be/platformkit/2010/1/android-1_5.owl>
    org.protege.owlapi.model.ProtegeOWLOntologyManager.callWithWriteLockUnchecked(ProtegeOWLOntologyManager.java:193)
    org.protege.owlapi.model.ProtegeOWLOntologyManager.applyChange(ProtegeOWLOntologyManager.java:137)
    org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:869)
    org.coode.owlapi.rdfxml.parser.TypeOntologyHandler.handleTriple(TypeOntologyHandler.java:68)
    org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handleStreaming(OWLRDFConsumer.java:1606)
    org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1581)
    org.semanticweb.owlapi.rdf.syntax.RDFParser.statementWithResourceValue(RDFParser.java:576)
    org.semanticweb.owlapi.rdf.syntax.RDFParser$NodeElement.startElement(RDFParser.java:868)
    org.semanticweb.owlapi.rdf.syntax.RDFParser$NodeElementList.startElement(RDFParser.java:797)
    org.semanticweb.owlapi.rdf.syntax.RDFParser.startElement(RDFParser.java:281)
    org.coode.owlapi.rdfxml.parser.RDFXMLParser$1.startElement(RDFXMLParser.java:92)
    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.startElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    javax.xml.parsers.SAXParser.parse(Unknown Source)
    org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:173)
    org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120)
    uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:667)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1084)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1112)
    org.coode.owlapi.rdfxml.parser.TPImportsHandler.handleTriple(TPImportsHandler.java:88)
    org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handleStreaming(OWLRDFConsumer.java:1626)
    org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1581)
    org.semanticweb.owlapi.rdf.syntax.RDFParser.statementWithResourceValue(RDFParser.java:576)
    org.semanticweb.owlapi.rdf.syntax.RDFParser$EmptyPropertyElement.startElement(RDFParser.java:1047)
    org.semanticweb.owlapi.rdf.syntax.RDFParser$PropertyElementList.startElement(RDFParser.java:924)
    org.semanticweb.owlapi.rdf.syntax.RDFParser.startElement(RDFParser.java:281)
    org.coode.owlapi.rdfxml.parser.RDFXMLParser$1.startElement(RDFXMLParser.java:92)
    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
    com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    javax.xml.parsers.SAXParser.parse(Unknown Source)
    org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:173)
    org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120)
    uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:683)
    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:317)
    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:180)
    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:174)
    org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:157)
    org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$2.actionPerformed(ProtegeWelcomeFrame.java:139)
    org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:102)
    org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
    org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:68)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)

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Re: error in opening ontology

Matthew Horridge-2
Administrator
Hi,

Please post questions about Protege 4 and OWL to the Protege 4 feedback list in future.

I tried to load the ontology that you pointed to but I can't find the import (http://soft.vub.ac.be/platformkit/2010/1/android.owl).   Anyway, I believe that the problem occurs because you have two different files in the imports closure containing ontologies with the same IRI.  i.e. FileA contains ontology X and FileB contains ontology X and they both get imported.  This problem shouldn't actually occur and is due to an issue with the OWL API.  Hopefully it will be fixed sometime in the near future, but for now, would it be possible for you to identify which files contain the problematic ontology?

Cheers,

Matthew




On 27 Nov 2011, at 06:10, Tanumeet Kaur Juneja wrote:

> Hi
> I am trying to open an ontology available at the link
>
> http://soft.vub.ac.be/viewvc/PlatformKit/platformkit-android/ontology/platformkit_2010_1/android-1_5.owl?view=log
>
> in protege 4.1 and getting the following list of errors..could any1 pls tell what could be the possible reason for these errors...
> Thanks a lot.
>
>
>
>
>
>
>
>
>
>
>
>
> Error 1 Logged at Sun Nov 27 19:36:25 IST 2011
> RuntimeException: java.lang.RuntimeException: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: <http://soft.vub.ac.be/platformkit/2010/1/android-1_5.owl>
>     org.protege.owlapi.model.ProtegeOWLOntologyManager.callWithWriteLockUnchecked(ProtegeOWLOntologyManager.java:193)
>     org.protege.owlapi.model.ProtegeOWLOntologyManager.applyChange(ProtegeOWLOntologyManager.java:137)
>     org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:869)
>     org.coode.owlapi.rdfxml.parser.TypeOntologyHandler.handleTriple(TypeOntologyHandler.java:68)
>     org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handleStreaming(OWLRDFConsumer.java:1606)
>     org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1581)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser.statementWithResourceValue(RDFParser.java:576)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser$NodeElement.startElement(RDFParser.java:868)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser$NodeElementList.startElement(RDFParser.java:797)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser.startElement(RDFParser.java:281)
>     org.coode.owlapi.rdfxml.parser.RDFXMLParser$1.startElement(RDFXMLParser.java:92)
>     com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.startElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
>     javax.xml.parsers.SAXParser.parse(Unknown Source)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:173)
>     org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120)
>     uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204)
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726)
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:667)
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1084)
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1112)
>     org.coode.owlapi.rdfxml.parser.TPImportsHandler.handleTriple(TPImportsHandler.java:88)
>     org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handleStreaming(OWLRDFConsumer.java:1626)
>     org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1581)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser.statementWithResourceValue(RDFParser.java:576)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser$EmptyPropertyElement.startElement(RDFParser.java:1047)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser$PropertyElementList.startElement(RDFParser.java:924)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser.startElement(RDFParser.java:281)
>     org.coode.owlapi.rdfxml.parser.RDFXMLParser$1.startElement(RDFXMLParser.java:92)
>     com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
>     com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
>     com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
>     javax.xml.parsers.SAXParser.parse(Unknown Source)
>     org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:173)
>     org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120)
>     uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204)
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726)
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:683)
>     org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:317)
>     org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:180)
>     org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:174)
>     org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:157)
>     org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$2.actionPerformed(ProtegeWelcomeFrame.java:139)
>     org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:102)
>     org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
>     org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:68)
>     java.awt.Component.processMouseEvent(Unknown Source)
>     javax.swing.JComponent.processMouseEvent(Unknown Source)
>     java.awt.Component.processEvent(Unknown Source)
>     java.awt.Container.processEvent(Unknown Source)
>     java.awt.Component.dispatchEventImpl(Unknown Source)
>     java.awt.Container.dispatchEventImpl(Unknown Source)
>     java.awt.Component.dispatchEvent(Unknown Source)
>     java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>     java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>     java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>     java.awt.Container.dispatchEventImpl(Unknown Source)
>     java.awt.Window.dispatchEventImpl(Unknown Source)
>     java.awt.Component.dispatchEvent(Unknown Source)
>     java.awt.EventQueue.dispatchEvent(Unknown Source)
>     java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>     java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>     java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>     java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>     java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>     java.awt.EventDispatchThread.run(Unknown Source)
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