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[protege-discussion] a simple questions about owl programming

Timothy Redmond tredmond at stanford.edu
Tue Nov 23 09:19:30 PST 2010


This is also a parser error.  It is not an error in your code as far as 
I can tell.  The Protege 3 OWL parser is parsing a file and it is having 
trouble dealing with some meta-modeling in the file.  Again if you have 
the ontology being parsed at this point I could provide some more 
information.

-Timothy


On 11/21/2010 07:51 PM, tingyu li wrote:
> Sorry, I forgot add "file:///" in front of my string uri. and I aslo 
> change file encodeing to UTF-8, and the error changed to:
>
>     SEVERE: Error at parsing triple:
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#\u4E60\u79F0
>     <http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#%5Cu4E60%5Cu79F0>
>     http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#alias --
>     java.lang.ClassCastException:
>     edu.stanford.smi.protegex.owl.model.impl.DefaultRDFProperty cannot
>     be cast to edu.stanford.smi.protege.model.Cls
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.AbstractStatefulTripleProcessor.getCls(AbstractStatefulTripleProcessor.java:106)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetType(TripleProcessorForResourceObjects.java:299)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetTypeAndCreation(TripleProcessorForResourceObjects.java:181)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:111)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:53)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessor.processTriple(TripleProcessor.java:43)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler.statement(ProtegeOWLParser.java:562)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.triple(XMLHandler.java:97)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.ParserSupport.triple(ParserSupport.java:240)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantDescription.aPredAndObj(WantDescription.java:101)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.theObject(WantPropertyElement.java:195)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.startElement(WantPropertyElement.java:123)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:132)
>         at
>     org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
>     Source)
>         at
>     org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.emptyElement(Unknown Source)
>         at
>     org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>         at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
>     Source)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106)
>         at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:143)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$1.invokeARP(ProtegeOWLParser.java:110)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(ProtegeOWLParser.java:276)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:190)
>         at
>     edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(JenaKnowledgeBaseFactory.java:204)
>         at
>     edu.stanford.smi.protege.model.Project.loadDomainKB(Project.java:1369)
>         at
>     edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Project.java:479)
>         at
>     edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.create(OwlProjectFromUriCreator.java:62)
>         at
>     edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(ProtegeOWL.java:84)
>         at
>     com.demo.application.classAndInstanceScanning.main(classAndInstanceScanning.java:23)
>
>     WARNING:     Frame with wrong Java type:
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#alias.
>     Expected: RDFSClass (or subclass), got:
>     edu.stanford.smi.protegex.owl.model.impl.DefaultRDFProperty --
>     AbstractStatefulTripleProcessor.getCls()
>     WARNING: Error at changing Java type of:
>     DefaultRDFProperty(http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#alias)
>     to DefaultOWLNamedClass -- java.lang.ClassCastException:
>     edu.stanford.smi.protegex.owl.model.impl.DefaultOWLNamedClass
>     cannot be cast to edu.stanford.smi.protege.model.Slot
>         at
>     edu.stanford.smi.protege.model.framestore.Record.replaceFrameReference(Record.java:116)
>         at
>     edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.replaceFrameKey(InMemoryFrameDb.java:286)
>         at
>     edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.replaceFrame(InMemoryFrameDb.java:556)
>         at
>     edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.replaceFrame(MergingNarrowFrameStore.java:629)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.AbstractStatefulTripleProcessor.swizzleFrame(AbstractStatefulTripleProcessor.java:153)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.AbstractStatefulTripleProcessor.getCls(AbstractStatefulTripleProcessor.java:97)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetType(TripleProcessorForResourceObjects.java:299)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetTypeAndCreation(TripleProcessorForResourceObjects.java:181)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:111)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:53)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessor.processTriple(TripleProcessor.java:43)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler.statement(ProtegeOWLParser.java:562)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.triple(XMLHandler.java:97)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.ParserSupport.triple(ParserSupport.java:240)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantDescription.aPredAndObj(WantDescription.java:101)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.theObject(WantPropertyElement.java:195)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.startElement(WantPropertyElement.java:123)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:132)
>         at
>     org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
>     Source)
>         at
>     org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.emptyElement(Unknown Source)
>         at
>     org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>         at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
>     Source)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106)
>         at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:143)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$1.invokeARP(ProtegeOWLParser.java:110)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(ProtegeOWLParser.java:276)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:190)
>         at
>     edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(JenaKnowledgeBaseFactory.java:204)
>         at
>     edu.stanford.smi.protege.model.Project.loadDomainKB(Project.java:1369)
>         at
>     edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Project.java:479)
>         at
>     edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.create(OwlProjectFromUriCreator.java:62)
>         at
>     edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(ProtegeOWL.java:84)
>         at
>     com.demo.application.classAndInstanceScanning.main(classAndInstanceScanning.java:23)
>
>     SEVERE: Error at parsing triple:
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#\u4EA6\u540D
>     <http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#%5Cu4EA6%5Cu540D>
>     http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#alias --
>     java.lang.ClassCastException:
>     edu.stanford.smi.protegex.owl.model.impl.DefaultRDFProperty cannot
>     be cast to edu.stanford.smi.protege.model.Cls
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.AbstractStatefulTripleProcessor.getCls(AbstractStatefulTripleProcessor.java:106)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetType(TripleProcessorForResourceObjects.java:299)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetTypeAndCreation(TripleProcessorForResourceObjects.java:181)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:111)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:53)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessor.processTriple(TripleProcessor.java:43)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler.statement(ProtegeOWLParser.java:562)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.triple(XMLHandler.java:97)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.ParserSupport.triple(ParserSupport.java:240)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantDescription.aPredAndObj(WantDescription.java:101)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.theObject(WantPropertyElement.java:195)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.startElement(WantPropertyElement.java:123)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:132)
>         at
>     org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
>     Source)
>         at
>     org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.emptyElement(Unknown Source)
>         at
>     org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>         at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
>     Source)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106)
>         at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:143)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$1.invokeARP(ProtegeOWLParser.java:110)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(ProtegeOWLParser.java:276)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:190)
>         at
>     edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(JenaKnowledgeBaseFactory.java:204)
>         at
>     edu.stanford.smi.protege.model.Project.loadDomainKB(Project.java:1369)
>         at
>     edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Project.java:479)
>         at
>     edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.create(OwlProjectFromUriCreator.java:62)
>         at
>     edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(ProtegeOWL.java:84)
>         at
>     com.demo.application.classAndInstanceScanning.main(classAndInstanceScanning.java:23)
>
>     WARNING:     Frame with wrong Java type:
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#alias.
>     Expected: RDFSClass (or subclass), got:
>     edu.stanford.smi.protegex.owl.model.impl.DefaultRDFProperty --
>     AbstractStatefulTripleProcessor.getCls()
>     WARNING: Error at changing Java type of:
>     DefaultRDFProperty(http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#alias)
>     to DefaultOWLNamedClass -- java.lang.ClassCastException:
>     edu.stanford.smi.protegex.owl.model.impl.DefaultOWLNamedClass
>     cannot be cast to edu.stanford.smi.protege.model.Slot
>         at
>     edu.stanford.smi.protege.model.framestore.Record.replaceFrameReference(Record.java:116)
>         at
>     edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.replaceFrameKey(InMemoryFrameDb.java:286)
>         at
>     edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.replaceFrame(InMemoryFrameDb.java:556)
>         at
>     edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.replaceFrame(MergingNarrowFrameStore.java:629)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.AbstractStatefulTripleProcessor.swizzleFrame(AbstractStatefulTripleProcessor.java:153)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.AbstractStatefulTripleProcessor.getCls(AbstractStatefulTripleProcessor.java:97)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetType(TripleProcessorForResourceObjects.java:299)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.handleSetTypeAndCreation(TripleProcessorForResourceObjects.java:181)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects$InternalTripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:111)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessorForResourceObjects.processTriple(TripleProcessorForResourceObjects.java:53)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.TripleProcessor.processTriple(TripleProcessor.java:43)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler.statement(ProtegeOWLParser.java:562)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.triple(XMLHandler.java:97)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.ParserSupport.triple(ParserSupport.java:240)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantDescription.aPredAndObj(WantDescription.java:101)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.theObject(WantPropertyElement.java:195)
>         at
>     com.hp.hpl.jena.rdf.arp.states.WantPropertyElement.startElement(WantPropertyElement.java:123)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:132)
>         at
>     org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
>     Source)
>         at
>     org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLNamespaceBinder.emptyElement(Unknown Source)
>         at
>     org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
>     Source)
>         at
>     org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown
>     Source)
>         at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>         at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
>     Source)
>         at
>     com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106)
>         at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:143)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$1.invokeARP(ProtegeOWLParser.java:110)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(ProtegeOWLParser.java:276)
>         at
>     edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:190)
>         at
>     edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(JenaKnowledgeBaseFactory.java:204)
>         at
>     edu.stanford.smi.protege.model.Project.loadDomainKB(Project.java:1369)
>         at
>     edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Project.java:479)
>         at
>     edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.create(OwlProjectFromUriCreator.java:62)
>         at
>     edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(ProtegeOWL.java:84)
>         at
>     com.demo.application.classAndInstanceScanning.main(classAndInstanceScanning.java:23)
>
>     SEVERE: Error at parsing triple:
>     http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#\u4EA6\u79F
>     <http://www.semanticweb.org/ontologies/2010/6/PNLN.owl#%5Cu4EA6%5Cu79F>
>
> ...
>
> 2010/11/22 tingyu li <li.hh190 at gmail.com <mailto:li.hh190 at gmail.com>>
>
>     guys, I have tried a lot of methods to figure out the problems,
>     but it still doesn't work, I'm pretty sure that this owl file have
>     some differences, because I have read them through a lot of codes.
>     and I also don't know what change I made on it. has anyone meet
>     the same problem?
>
>     2010/11/20 tingyu li <li.hh190 at gmail.com <mailto:li.hh190 at gmail.com>>
>
>         hi Timothy,
>
>         I change an other owl files to load as the same way as son,
>         but It failed, It must be caused  by the owl file error, which
>         I can't figure out.
>         so I use the Progtege api to load the same file, the code:
>
>             String uri = "locationpath";
>                     OWLModel owlModel =
>             ProtegeOWL.createJenaOWLModelFromURI(uri);
>
>                     Collection classes =
>             owlModel.getUserDefinedOWLNamedClasses();
>
>                     for (Iterator it = classes.iterator();
>             it.hasNext();) {
>                         OWLNamedClass cls = (OWLNamedClass) it.next();
>                         Collection instances = cls.getInstances(false);
>                         System.out.println("Class " +
>             cls.getBrowserText() + " (" + instances.size() + ")");
>                         for (Iterator jt = instances.iterator();
>             jt.hasNext();) {
>                             OWLIndividual individual = (OWLIndividual)
>             jt.next();
>
>                             System.out.println(" - " +
>             individual.getBrowserText());
>                         }
>                     }
>
>          it still failed, and the error message, which is much similar
>         with the error Propervalue class made:
>
>             Protege 3.4.4 Build 579, JVM 1.6.0_18-b07, memory=259M,
>             Windows 7, encoding=UTF-8, language=zh, country=CN
>             WARNING: Plugins directory not found:
>             D:\workspace\lastprotege\plugins --
>             PluginUtilities.findPluginsDirectory()
>             WARNING: [Local Folder Repository] The specified file must
>             be a directory.
>             (D:\workspace\lastprotege\plugins\edu.stanford.smi.protegex.owl)
>             -- LocalFolderRepository.update()
>             SEVERE: Error at loading file
>             C://Users//LiTingyu//ontologies//resultcollection.owl -- null
>                 at
>             edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:174)
>                 at
>             edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(JenaKnowledgeBaseFactory.java:204)
>                 at
>             edu.stanford.smi.protege.model.Project.loadDomainKB(Project.java:1369)
>                 at
>             edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Project.java:479)
>                 at
>             edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.create(OwlProjectFromUriCreator.java:62)
>                 at
>             edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(ProtegeOWL.java:84)
>                 at
>             com.demo.application.classAndInstanceScanning.main(classAndInstanceScanning.java:22)
>             Caused by: java.net.MalformedURLException: unknown protocol: c
>                 at java.net.URL.<init>(Unknown Source)
>                 at java.net.URL.<init>(Unknown Source)
>                 at java.net.URL.<init>(Unknown Source)
>                 at java.net.URI.toURL(Unknown Source)
>                 at
>             edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:172)
>                 ... 6 more
>
>             WARNING: Error found
>             edu.stanford.smi.protege.util.MessageError at 175d6ab --
>             ProtegeOWL.handleErrors()
>             WARNING: Error found
>             edu.stanford.smi.protege.util.MessageError at 160a26f --
>             ProtegeOWL.handleErrors()
>             Exception in thread "main" java.lang.NullPointerException
>                 at
>             com.demo.application.classAndInstanceScanning.main(classAndInstanceScanning.java:38)
>
>
>
>         2010/11/19 Timothy Redmond <tredmond at stanford.edu
>         <mailto:tredmond at stanford.edu>>
>
>             On 11/18/2010 08:53 AM, tingyu li wrote:
>>             Hi Timothy,
>>             it's really very in detail, and works. thank you very much.
>>             And another problem is how to scan the all properties
>>             that the individual has? I want get these properties and
>>             values as a pair...
>
>             In the Protege 3 OWL api you use
>             getPossibleRDFProperties.  In the Manchester OWL api,
>             OWLIndividual has a method called getObjectPropertyValues.
>
>             -Timothy
>
>
>
>>
>>             2010/11/19 Timothy Redmond <tredmond at stanford.edu
>>             <mailto:tredmond at stanford.edu>>
>>
>>
>>                 The code you had essentially works except that the line
>>
>>
>>>                              OWLObjectProperty individual = (OWLObjectProperty) jt.next();
>>
>>                 is unlikely to succeed.  You would expect the next
>>                 value to be an OWLIndividual (or a literal) not an
>>                 object property.
>>
>>
>>>                 /WARNING: Invalid frame type:
>>>                 DefaultOWLIndividual(http://www.semanticweb.org/ontologies/2010/0/family.owl#Jim
>>>                 of
>>>                 [DefaultOWLNamedClass(http://www.w3.org/2002/07/owl#Thing),
>>>                 DefaultOWLNamedClass(http://www.semanticweb.org/ontologies/2010/0/family.owl#male_family_member),
>>>                 DefaultRDFSNamedClass(http://www.w3.org/2002/07/owl#NamedIndividual)
>>>                 <http://www.w3.org/2002/07/owl#NamedIndividual%29>])
>>>                 -- AbstractRedirectingDispatch.getDirectOwnSlotValues()
>>>                 Exception in thread "main"
>>>                 java.lang.IllegalArgumentException: null slot/
>>
>>                 The first warning is weird but the exception means
>>                 what it says.  Your owlModel does not have a hasSon
>>                 object property in it so objectProp is null.
>>
>>
>>>                 and I have take a look at owlapi, it's really more
>>>                 direct to handle. but after I checked these code
>>>                 sample on the website, I found that these codes only
>>>                 do some actions about class. but my target is
>>>                 individual.
>>
>>                 The "Classes and instances" example from [1] has
>>                 individuals.  To write your code in the owl api you
>>                 simply put:
>>
>>                      OWLNamedIndividual jim = factory.getOWLNamedIndividual(":jim", prefixManager);
>>                      OWLObjectProperty hasSon = factory.getOWLObjectProperty(":hasSon", prefixManager);
>>
>>                      for (OWLIndividual son : jim.getObjectPropertyValues(hasSon, ontology)) {
>>                          System.out.println(" - " + son);
>>                      }
>>
>>
>>                 -Timothy
>>
>>
>>                 [1]http://owlapi.sourceforge.net/documentation.html
>>
>>
>>                 On 11/18/2010 06:55 AM, tingyu li wrote:
>>>                 thanks for you guys response. and I have take a look
>>>                 at owlapi, it's really more direct to handle. but
>>>                 after I checked these code sample on the website, I
>>>                 found that these codes only do some actions about
>>>                 class. but my target is individual. how to get
>>>                 specific individual's object property assertions is
>>>                 my purpose.
>>>                 And at the same time, I find a simple way that maybe
>>>                 can get this, the code is :
>>>
>>>                             OWLIndividual ind =
>>>                     owlModel.getOWLIndividual("Jim");
>>>                             OWLObjectProperty objectProp =
>>>                     owlModel.getOWLObjectProperty("hasSon");
>>>                             Collection values =
>>>                     ind.getPropertyValues(objectProp);
>>>                             for (Iterator jt = values.iterator();
>>>                     jt.hasNext();) {
>>>                                 OWLObjectProperty individual =
>>>                     (OWLObjectProperty) jt.next();
>>>                                 System.out.println(" - " +
>>>                     individual.getBrowserText());
>>>                             }
>>>
>>>                 but error message returned said:
>>>                 /WARNING: Invalid frame type:
>>>                 DefaultOWLIndividual(http://www.semanticweb.org/ontologies/2010/0/family.owl#Jim
>>>                 of
>>>                 [DefaultOWLNamedClass(http://www.w3.org/2002/07/owl#Thing),
>>>                 DefaultOWLNamedClass(http://www.semanticweb.org/ontologies/2010/0/family.owl#male_family_member),
>>>                 DefaultRDFSNamedClass(http://www.w3.org/2002/07/owl#NamedIndividual)
>>>                 <http://www.w3.org/2002/07/owl#NamedIndividual%29>])
>>>                 -- AbstractRedirectingDispatch.getDirectOwnSlotValues()
>>>                 Exception in thread "main"
>>>                 java.lang.IllegalArgumentException: null slot/
>>>                 it seems that this code just can handle the old
>>>                 version proj, so is there any replacement of 4.0 for
>>>                 the same target?
>>>
>>>                 In the other hand,  as thomas mentioned,
>>>
>>>                     All of the assertion information would be
>>>                     retrieved in the form of different kinds of
>>>                     axioms that you would get for a particular
>>>                     individual (like Jim) by calling the method with
>>>                     signature:
>>>
>>>                     OWLOntology.getAxioms(
>>>
>>>                         OWLIndividual)
>>>
>>>                         and then filtering the results in to
>>>                         different classes of axiom such as
>>>
>>>                         OWLPropertyAssertionAxiom which supports
>>>                         getProperty() and getObject() to tell you
>>>                         which property and value it has.
>>>
>>>                         The usages would seem to be returned by
>>>
>>>                         OWLOntology.getReferencingAxioms(OWLEntity)
>>>
>>>                 I will appreciate if you can give me code samples
>>>                 about how to drive them.
>>>
>>>                 thx a lot!
>>>
>>>                 2010/11/18 Thomas Russ <tar at isi.edu
>>>                 <mailto:tar at isi.edu>>
>>>
>>>
>>>                     On Nov 17, 2010, at 7:20 AM, tingyu li wrote:
>>>
>>>                         hi Thomas, thanks for your response. but I
>>>                         still very confused by these methods...and I
>>>                         have read all the samples posted on the
>>>                         website, but I don't find any solutions for
>>>                         my problems, a very similar question is
>>>                         about query all resources that have a
>>>                         certain property value. the code on website
>>>                         is like this:
>>>                         RDFProperty subClassOfProperty =
>>>                         owlModel.getRDFProperty(RDFSNames.Slot.SUB_CLASS_OF);
>>>
>>>                         OWLNamedClass owlThingClass =
>>>                         owlModel.getOWLThingClass();
>>>                         Collection results =
>>>                         owlModel.getRDFResourcesWithPropertyValue(subClassOfProperty,
>>>                         owlThingClass);
>>>                         System.out.println("Subclasses of owl:Thing:");
>>>
>>>                         for (Iterator it = results.iterator();
>>>                         it.hasNext();) {
>>>                            RDFResource resource = (RDFResource)
>>>                         it.next();
>>>                            System.out.println(" - " +
>>>                         resource.getBrowserText());
>>>                         }
>>>                         but, actually, there are no slot on the new
>>>                         version owl files. and I think RDFProperty
>>>                         is not very fit for my file. by the way, I
>>>                         use protege 4.0 to develop a owl file and
>>>                         save it as format: RDF/XML. the file  is
>>>                         like this:
>>>
>>>
>>>                     You have to look at the class hierarchy in the
>>>                     Java code.
>>>                     OWLObjectProperty and OWLIndividual are all
>>>                     subclasses of RDFPropery and RDFResource, so
>>>                     those methods will be applicable.
>>>
>>>                     But if you are going to be using Protege 4, then
>>>                     you should be using the OWLAPI to work with the
>>>                     ontology rather than the Protege-OWL API.  That
>>>                     is the underlying code that the Protege 4 code
>>>                     uses.   OWLAPIv3 is used in Protege 4.1
>>>
>>>                     So the place to start for OWLAPI programming are
>>>                     the following documents:
>>>
>>>                     http://owlapi.sourceforge.net/documentation.html
>>>
>>>                     All of the assertion information would be
>>>                     retrieved in the form of different kinds of
>>>                     axioms that you would get for a particular
>>>                     individual (like Jim) by calling the method with
>>>                     signature:
>>>
>>>                       OWLOntology.getAxioms(OWLIndividual)
>>>
>>>                     and then filtering the results in to different
>>>                     classes of axiom such as
>>>
>>>                       OWLPropertyAssertionAxiom which supports
>>>                     getProperty() and getObject() to tell you which
>>>                     property and value it has.
>>>
>>>                     The usages would seem to be returned by
>>>
>>>                       OWLOntology.getReferencingAxioms(OWLEntity)
>>>
>>>
>>>
>>>
>>>                         <owl:ObjectProperty
>>>                         rdf:about="http://www.semanticweb.org/ontologies/2010/0/family.owl#isUncleOf">
>>>                         <rdfs:range
>>>                         rdf:resource="http://www.semanticweb.org/ontologies/2010/0/family.owl#family_member"/>
>>>                         <rdfs:domain
>>>                         rdf:resource="http://www.semanticweb.org/ontologies/2010/0/family.owl#male_family_member"/>
>>>                         </owl:ObjectProperty>
>>>                         I want get the similar result as the probem
>>>                         I described above. in other words, if I
>>>                         click Jim as the picture, I can get the
>>>                         result as the rigt part of the picture
>>>                         displayed, Usage and Property assertions:Jim
>>>
>>>                         thanks.
>>>
>>>
>>>                     _______________________________________________
>>>                     protege-discussion mailing list
>>>                     protege-discussion at lists.stanford.edu
>>>                     <mailto:protege-discussion at lists.stanford.edu>
>>>                     https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>
>>>                     Instructions for unsubscribing:
>>>                     http://protege.stanford.edu/doc/faq.html#01a.03
>>>
>>>
>>>
>>>
>>>                 -- 
>>>                 Li
>>>
>>>
>>>                 _______________________________________________
>>>                 protege-discussion mailing list
>>>                 protege-discussion at lists.stanford.edu  <mailto:protege-discussion at lists.stanford.edu>
>>>                 https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>
>>>                 Instructions for unsubscribing:http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>>                 _______________________________________________
>>                 protege-discussion mailing list
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>>                 <mailto:protege-discussion at lists.stanford.edu>
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>>
>>                 Instructions for unsubscribing:
>>                 http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>>
>>
>>             -- 
>>             Li Tingyu
>>             ==========================================================
>>             Mobile (China): +(86) 136 6173 2368
>>             Computer Science Department Shanghai JiaoTong University
>>             Address: No. 800 Dongchuan Road, Shanghai China, 200240
>>             ==========================================================
>>
>>
>>             _______________________________________________
>>             protege-discussion mailing list
>>             protege-discussion at lists.stanford.edu  <mailto:protege-discussion at lists.stanford.edu>
>>             https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>>             Instructions for unsubscribing:http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>             _______________________________________________
>             protege-discussion mailing list
>             protege-discussion at lists.stanford.edu
>             <mailto:protege-discussion at lists.stanford.edu>
>             https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
>             Instructions for unsubscribing:
>             http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
>
>         -- 
>         Li
>
>
>
>
>     -- 
>     Li
>
>
> _______________________________________________
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