Error: Protege 4.0´s Ontology in Protege 4.1.0

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Error: Protege 4.0´s Ontology in Protege 4.1.0

Julio Nardi
Hello!

I´m trying to open an ontology in Protege 4.1.0, but I´m getting some problems.

This ontology was made using Protege 4.0.

Below, the error trace is showed.

Can you help me?

Thanks,
Julio.


Error 7 Logged at Mon Mar 08 10:16:47 BRT 2010
NullPointerException: null
    org.semanticweb.owlapi.util.HashCode.visit(HashCode.java:626)
    uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:105)
    org.semanticweb.owlapi.util.HashCode.hashCode(HashCode.java:43)
    uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.hashCode(OWLObjectImpl.java:147)
    java.util.HashMap.put(Unknown Source)
    java.util.HashSet.add(Unknown Source)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:1728)
    org.semanticweb.owlapi.model.AddOntologyAnnotation.accept(AddOntologyAnnotation.java:70)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:1638)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:340)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:408)
    org.coode.owlapi.owlxmlparser.OWLOntologyHandler.handleChild(OWLOntologyHandler.java:72)
    org.coode.owlapi.owlxmlparser.OWLAnnotationElementHandler.endElement(OWLAnnotationElementHandler.java:57)
    org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:838)
    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source)
    javax.xml.parsers.SAXParser.parse(Unknown Source)
    org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:55)
    uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:312)
    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
    org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
    org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:217)
    org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    javax.swing.AbstractButton.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    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: Protege 4.0´s Ontology in Protege 4.1.0

Timothy Redmond

Is there any possibility that you could send the ontology (out of line
if need be)?  The exception is saying that there was some problem
parsing an annotation and at some point the annotation property became
null.  But if we had the file we could tell you more.

Alternatively there is an owl validator that you could use:

  http://www.mygrid.org.uk/OWL/Validator

-Timothy

Julio Nardi wrote:

> Hello!
>
> I´m trying to open an ontology in Protege 4.1.0, but I´m getting some
> problems.
>
> This ontology was made using Protege 4.0.
>
> Below, the error trace is showed.
>
> Can you help me?
>
> Thanks,
> Julio.
>
>
> Error 7 Logged at Mon Mar 08 10:16:47 BRT 2010
> NullPointerException: null
>     org.semanticweb.owlapi.util.HashCode.visit(HashCode.java:626)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:105)
>     org.semanticweb.owlapi.util.HashCode.hashCode(HashCode.java:43)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.hashCode(OWLObjectImpl.java:147)
>     java.util.HashMap.put(Unknown Source)
>     java.util.HashSet.add(Unknown Source)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:1728)
>    
> org.semanticweb.owlapi.model.AddOntologyAnnotation.accept(AddOntologyAnnotation.java:70)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:1638)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:340)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:408)
>    
> org.coode.owlapi.owlxmlparser.OWLOntologyHandler.handleChild(OWLOntologyHandler.java:72)
>    
> org.coode.owlapi.owlxmlparser.OWLAnnotationElementHandler.endElement(OWLAnnotationElementHandler.java:57)
>    
> org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:838)
>    
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown
> Source)
>    
> com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown
> Source)
>    
> com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(Unknown
> Source)
>    
> com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(Unknown
> Source)
>    
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown
> Source)
>    
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown
> Source)
>     javax.xml.parsers.SAXParser.parse(Unknown Source)
>     org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:55)
>    
> uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
>    
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
>    
> org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:312)
>    
> org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>    
> org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
>    
> org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
>     org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:217)
>    
> org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
>     javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>     javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>     javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>     javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>     javax.swing.AbstractButton.doClick(Unknown Source)
>     javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>    
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
> Source)
>     java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
>     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)
> ---------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>  

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Re: Error: Protege 4.0´s Ontology in Protege 4.1.0

Matthew Horridge
Further to what Tim said,

There's an OWL 2 (more up to date) validator at:

http://owl.cs.manchester.ac.uk/validator/

Cheers,

Matthew

On 8 Mar 2010, at 13:49, Timothy Redmond wrote:

>
> Is there any possibility that you could send the ontology (out of line if need be)?  The exception is saying that there was some problem parsing an annotation and at some point the annotation property became null.  But if we had the file we could tell you more.
>
> Alternatively there is an owl validator that you could use:
>
> http://www.mygrid.org.uk/OWL/Validator
>
> -Timothy
>
> Julio Nardi wrote:
>> Hello!
>>
>> I´m trying to open an ontology in Protege 4.1.0, but I´m getting some problems.
>>
>> This ontology was made using Protege 4.0.
>>
>> Below, the error trace is showed.
>>
>> Can you help me?
>>
>> Thanks,
>> Julio.
>>
>>
>> Error 7 Logged at Mon Mar 08 10:16:47 BRT 2010
>> NullPointerException: null
>>    org.semanticweb.owlapi.util.HashCode.visit(HashCode.java:626)
>>    uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:105)
>>    org.semanticweb.owlapi.util.HashCode.hashCode(HashCode.java:43)
>>    uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.hashCode(OWLObjectImpl.java:147)
>>    java.util.HashMap.put(Unknown Source)
>>    java.util.HashSet.add(Unknown Source)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:1728)
>>    org.semanticweb.owlapi.model.AddOntologyAnnotation.accept(AddOntologyAnnotation.java:70)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:1638)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:340)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:408)
>>    org.coode.owlapi.owlxmlparser.OWLOntologyHandler.handleChild(OWLOntologyHandler.java:72)
>>    org.coode.owlapi.owlxmlparser.OWLAnnotationElementHandler.endElement(OWLAnnotationElementHandler.java:57)
>>    org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:838)
>>    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source)
>>    javax.xml.parsers.SAXParser.parse(Unknown Source)
>>    org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:55)
>>    uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
>>    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:312)
>>    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>>    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
>>    org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
>>    org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:217)
>>    org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
>>    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>>    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>>    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>    javax.swing.AbstractButton.doClick(Unknown Source)
>>    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>>    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
>>    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
>>    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)
>> ---------------------------------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>  
>
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Re: Error: Protege 4.0´s Ontology in Protege 4.1.0

Julio Nardi
Hello!

I´ve done some tests and I ´ve found that the problem was the "annotations".

So, It was necessary to delete all of them. Thus, the ontology was validated (by the OWL Validator) and, then, it was opened in the Protege 4.1.0.

But, there is an interesting thing: If I create an annotation in the ontology using Protege 4.1.0, the ontology is not validated by the OWL Validator.

So, now I am trying to found how create annotation that can be validated by the parser.

Thank you very much!
Julio.


On Mon, Mar 8, 2010 at 11:06 AM, Matthew Horridge <[hidden email]> wrote:
Further to what Tim said,

There's an OWL 2 (more up to date) validator at:

http://owl.cs.manchester.ac.uk/validator/

Cheers,

Matthew

On 8 Mar 2010, at 13:49, Timothy Redmond wrote:

>
> Is there any possibility that you could send the ontology (out of line if need be)?  The exception is saying that there was some problem parsing an annotation and at some point the annotation property became null.  But if we had the file we could tell you more.
>
> Alternatively there is an owl validator that you could use:
>
> http://www.mygrid.org.uk/OWL/Validator
>
> -Timothy
>
> Julio Nardi wrote:
>> Hello!
>>
>> I´m trying to open an ontology in Protege 4.1.0, but I´m getting some problems.
>>
>> This ontology was made using Protege 4.0.
>>
>> Below, the error trace is showed.
>>
>> Can you help me?
>>
>> Thanks,
>> Julio.
>>
>>
>> Error 7 Logged at Mon Mar 08 10:16:47 BRT 2010
>> NullPointerException: null
>>    org.semanticweb.owlapi.util.HashCode.visit(HashCode.java:626)
>>    uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:105)
>>    org.semanticweb.owlapi.util.HashCode.hashCode(HashCode.java:43)
>>    uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.hashCode(OWLObjectImpl.java:147)
>>    java.util.HashMap.put(Unknown Source)
>>    java.util.HashSet.add(Unknown Source)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:1728)
>>    org.semanticweb.owlapi.model.AddOntologyAnnotation.accept(AddOntologyAnnotation.java:70)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:1638)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:340)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:408)
>>    org.coode.owlapi.owlxmlparser.OWLOntologyHandler.handleChild(OWLOntologyHandler.java:72)
>>    org.coode.owlapi.owlxmlparser.OWLAnnotationElementHandler.endElement(OWLAnnotationElementHandler.java:57)
>>    org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:838)
>>    com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
>>    com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source)
>>    javax.xml.parsers.SAXParser.parse(Unknown Source)
>>    org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:55)
>>    uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
>>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
>>    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:312)
>>    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>>    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
>>    org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
>>    org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:217)
>>    org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
>>    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>>    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>>    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>    javax.swing.AbstractButton.doClick(Unknown Source)
>>    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>>    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
>>    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
>>    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)
>> ---------------------------------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>
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Re: Error: Protege 4.0´s Ontology in Protege 4.1.0

Timothy Redmond


> But, there is an interesting thing: If I create an annotation in the
> ontology using Protege 4.1.0, the ontology is not validated by the OWL
> Validator.

If you simply create an ontology, create some classes and add some
annotations then the ontology should validate fine with the wonderweb
owl validator [1].  However that OWL Validator will only understand OWL
1 ontologies so if you use any OWL 2 constructs then it will not
validate.

This is the advantage of the validator that Matthew suggested [2].  This
validator will also handle any OWL 2.0 constructs that you could use.

-Timothy


[1] http://www.mygrid.org.uk/OWL/Validator
[2] http://owl.cs.manchester.ac.uk/validator/

On Mon, 2010-03-08 at 13:57 -0300, Julio Nardi wrote:

> Hello!
>
> I´ve done some tests and I ´ve found that the problem was the
> "annotations".
>
> So, It was necessary to delete all of them. Thus, the ontology was
> validated (by the OWL Validator) and, then, it was opened in the
> Protege 4.1.0.
>
> But, there is an interesting thing: If I create an annotation in the
> ontology using Protege 4.1.0, the ontology is not validated by the OWL
> Validator.
>
> So, now I am trying to found how create annotation that can be
> validated by the parser.
>
> Thank you very much!
> Julio.
>
>
> On Mon, Mar 8, 2010 at 11:06 AM, Matthew Horridge
> <[hidden email]> wrote:
>         Further to what Tim said,
>        
>         There's an OWL 2 (more up to date) validator at:
>        
>         http://owl.cs.manchester.ac.uk/validator/
>        
>         Cheers,
>        
>         Matthew
>        
>        
>         On 8 Mar 2010, at 13:49, Timothy Redmond wrote:
>        
>         >
>         > Is there any possibility that you could send the ontology
>         (out of line if need be)?  The exception is saying that there
>         was some problem parsing an annotation and at some point the
>         annotation property became null.  But if we had the file we
>         could tell you more.
>         >
>         > Alternatively there is an owl validator that you could use:
>         >
>         > http://www.mygrid.org.uk/OWL/Validator
>         >
>         > -Timothy
>         >
>         > Julio Nardi wrote:
>         >> Hello!
>         >>
>         >> I´m trying to open an ontology in Protege 4.1.0, but I´m
>         getting some problems.
>         >>
>         >> This ontology was made using Protege 4.0.
>         >>
>         >> Below, the error trace is showed.
>         >>
>         >> Can you help me?
>         >>
>         >> Thanks,
>         >> Julio.
>         >>
>         >>
>         >> Error 7 Logged at Mon Mar 08 10:16:47 BRT 2010
>         >> NullPointerException: null
>         >>
>          org.semanticweb.owlapi.util.HashCode.visit(HashCode.java:626)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:105)
>         >>
>          org.semanticweb.owlapi.util.HashCode.hashCode(HashCode.java:43)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.hashCode(OWLObjectImpl.java:147)
>         >>    java.util.HashMap.put(Unknown Source)
>         >>    java.util.HashSet.add(Unknown Source)
>         >>    uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl
>         $OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:1728)
>         >>
>          org.semanticweb.owlapi.model.AddOntologyAnnotation.accept(AddOntologyAnnotation.java:70)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:1638)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:340)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:408)
>         >>
>          org.coode.owlapi.owlxmlparser.OWLOntologyHandler.handleChild(OWLOntologyHandler.java:72)
>         >>
>          org.coode.owlapi.owlxmlparser.OWLAnnotationElementHandler.endElement(OWLAnnotationElementHandler.java:57)
>         >>
>          org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:838)
>         >>
>          com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown Source)
>         >>
>          com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
>         >>
>          com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
>         >>
>          com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
>         >>
>          com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
>         >>
>          com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$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.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:55)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
>         >>
>          uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
>         >>
>          org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:312)
>         >>
>          org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>         >>
>          org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
>         >>
>          org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
>         >>
>          org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:217)
>         >>
>          org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
>         >>    javax.swing.AbstractButton.fireActionPerformed(Unknown
>         Source)
>         >>    javax.swing.AbstractButton
>         $Handler.actionPerformed(Unknown Source)
>         >>
>          javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
>         Source)
>         >>    javax.swing.DefaultButtonModel.setPressed(Unknown
>         Source)
>         >>    javax.swing.AbstractButton.doClick(Unknown Source)
>         >>    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown
>         Source)
>         >>    javax.swing.plaf.basic.BasicMenuItemUI
>         $Handler.mouseReleased(Unknown Source)
>         >>    java.awt.AWTEventMulticaster.mouseReleased(Unknown
>         Source)
>         >>    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)
>         >>
>         ---------------------------------------------------------------------------------------------------
>         >>
>         >>
>         >>
>         ------------------------------------------------------------------------
>         >>
>         >> _______________________________________________
>         >> p4-feedback mailing list
>         >> [hidden email]
>         >> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>         >>
>         >
>         > _______________________________________________
>         > p4-feedback mailing list
>         > [hidden email]
>         > https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>        
>         _______________________________________________
>         p4-feedback mailing list
>         [hidden email]
>         https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>        
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: Error: Protege 4.0´s Ontology in Protege 4.1.0 [SEC=UNCLASSIFIED]

Paul Murray
In reply to this post by Matthew Horridge
Blow me down! It Works!

If I read the following in,  Hermit correctly infers my bike, quad and truck are two, four, and other wheeled vehicles, and that badvehicle is a subclass of Nothing.

The only trick is that there isn't really a gui for the class expressions, you have to edit it manually in this form
        not (wheelCount some  not ({"4"^^nonNegativeInteger}))
which (I assume) is manchester syntax.



Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(foo:=<http://foo.bar/voc#>)
Ontology(
  <http://foo.bar/voc>
Declaration(Class(foo:WheeledVehicle))
Declaration(Class(foo:TwoWheeledVehicle))
Declaration(Class(foo:FourWheeledVehicle))
Declaration(Class(foo:OtherWheeledVehicle))
SubClassOf(foo:TwoWheeledVehicle foo:WheeledVehicle)
SubClassOf(foo:FourWheeledVehicle foo:WheeledVehicle)
SubClassOf(foo:OtherWheeledVehicle foo:WheeledVehicle)
Declaration(DataProperty(foo:wheelCount))
Declaration(NamedIndividual(foo:MyBike))
Declaration(NamedIndividual(foo:MyQuad))
Declaration(NamedIndividual(foo:MyTruck))
Declaration(NamedIndividual(foo:BadVehicle))
FunctionalDataProperty(foo:wheelCount)
DataPropertyRange(foo:wheelCount xsd:nonNegativeInteger)
DataPropertyAssertion(foo:wheelCount foo:MyBike "2"^^xsd:nonNegativeInteger)
DataPropertyAssertion(foo:wheelCount foo:MyQuad "4"^^xsd:nonNegativeInteger)
DataPropertyAssertion(foo:wheelCount foo:MyTruck "18"^^xsd:nonNegativeInteger)
DataPropertyAssertion(foo:wheelCount foo:BadVehicle "2"^^xsd:nonNegativeInteger)
ClassAssertion(foo:FourWheeledVehicle foo:BadVehicle)
EquivalentClasses(foo:TwoWheeledVehicle DataHasValue(foo:wheelCount "2"^^xsd:nonNegativeInteger))
EquivalentClasses(foo:TwoWheeledVehicle ObjectComplementOf(DataSomeValuesFrom(foo:wheelCount DataComplementOf(DataOneOf("2"^^xsd:nonNegativeInteger)))))
EquivalentClasses(foo:FourWheeledVehicle DataHasValue(foo:wheelCount "4"^^xsd:nonNegativeInteger))
EquivalentClasses(foo:FourWheeledVehicle ObjectComplementOf(DataSomeValuesFrom(foo:wheelCount DataComplementOf(DataOneOf("4"^^xsd:nonNegativeInteger)))))
EquivalentClasses(foo:OtherWheeledVehicle DataSomeValuesFrom(foo:wheelCount DataComplementOf(DataOneOf("2"^^xsd:nonNegativeInteger "4"^^xsd:nonNegativeInteger))))
)


On 09/03/2010, at 1:06 AM, Matthew Horridge wrote:

> Further to what Tim said,
>
> There's an OWL 2 (more up to date) validator at:
>
> http://owl.cs.manchester.ac.uk/validator/
>
> Cheers,
>
> Matthew
>
> On 8 Mar 2010, at 13:49, Timothy Redmond wrote:
>
>>
>> Is there any possibility that you could send the ontology (out of line if need be)?  The exception is saying that there was some problem parsing an annotation and at some point the annotation property became null.  But if we had the file we could tell you more.
>>
>> Alternatively there is an owl validator that you could use:
>>
>> http://www.mygrid.org.uk/OWL/Validator
>>
>> -Timothy
>>
>> Julio Nardi wrote:
>>> Hello!
>>>
>>> I´m trying to open an ontology in Protege 4.1.0, but I´m getting some problems.
>>>
>>> This ontology was made using Protege 4.0.
>>>
>>> Below, the error trace is showed.
>>>
>>> Can you help me?
>>>
>>> Thanks,
>>> Julio.
>>>
>>>
>>> Error 7 Logged at Mon Mar 08 10:16:47 BRT 2010
>>> NullPointerException: null
>>>   org.semanticweb.owlapi.util.HashCode.visit(HashCode.java:626)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:105)
>>>   org.semanticweb.owlapi.util.HashCode.hashCode(HashCode.java:43)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.hashCode(OWLObjectImpl.java:147)
>>>   java.util.HashMap.put(Unknown Source)
>>>   java.util.HashSet.add(Unknown Source)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:1728)
>>>   org.semanticweb.owlapi.model.AddOntologyAnnotation.accept(AddOntologyAnnotation.java:70)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:1638)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:340)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:408)
>>>   org.coode.owlapi.owlxmlparser.OWLOntologyHandler.handleChild(OWLOntologyHandler.java:72)
>>>   org.coode.owlapi.owlxmlparser.OWLAnnotationElementHandler.endElement(OWLAnnotationElementHandler.java:57)
>>>   org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:838)
>>>   com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(Unknown Source)
>>>   com.sun.org.apache.xerces.internal.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
>>>   com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
>>>   com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
>>>   com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
>>>   com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source)
>>>   javax.xml.parsers.SAXParser.parse(Unknown Source)
>>>   org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:55)
>>>   uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
>>>   uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
>>>   org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:312)
>>>   org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>>>   org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
>>>   org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
>>>   org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:217)
>>>   org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
>>>   javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>>   javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>>>   javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>>>   javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>>   javax.swing.AbstractButton.doClick(Unknown Source)
>>>   javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>>>   javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
>>>   java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
>>>   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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