owl API backwards incompatible ? Can't open P4.01 owl file after saving it with P4.1beta (new owl API)

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owl API backwards incompatible ? Can't open P4.01 owl file after saving it with P4.1beta (new owl API)

Daniel Schober
Dear Protege Programmers,

We have recently moved to edit our dco.owl file (attached or see on http://www.imbi.uni-freiburg.de/~schober/dco_owlDoc/dco.owl)  with P.4.1.0 (Alpha, build 102), and have discovered that once saved with P.4.1Alpha it can not be opened by P.4.0.2. anymore, error messages and cmd out, see below. We work on a windows  PC.

Is this a backwards incompatability from the new owl 2 Ver 3 API  to the older owl API as used in P 4.0.2 ? How can I still edit the file in P4.0.2. and also in P4.1 ?
(The main reason we want P 4.1Alpha is that Hermit is so much faster. Maybe this should be made the standard default reasoner for P3.x and P4.0.x as well...The reason we need P4.0.2. is that the OwoDoc plugin does not work in P 4.1.0 ).

Is there a way I can generate an OwlDocHTML serialisation from my owl 2 (P4.1.0 saved) ontology ?

Cheers,
    Daniel Schober.

---

RDFXML Parser Error:
org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.

Stack Trace:
org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
-----------------------------------------------------------------------------------------
org.coode.owl.rdfxml.parser.OWLRDFXMLParserSAXException: org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
    at org.coode.owl.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:90)
    at uk.ac.manchester.cs.owl.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:159)
    at uk.ac.manchester.cs.owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:461)
    at uk.ac.manchester.cs.owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:424)
    at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntology(OWLModelManagerImpl.java:328)
    at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:390)
    at org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:147)
    at org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKit.java:135)
    at org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(ProtegeManager.java:173)
    at org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$5.actionPerformed(ProtegeWelcomeFrame.java:235)
    at org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:97)
    at org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
    at org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:63)
    at java.awt.Component.processMouseEvent(Component.java:6263)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
    at java.awt.Component.processEvent(Component.java:6028)
    at java.awt.Container.processEvent(Container.java:2041)
    at java.awt.Component.dispatchEventImpl(Component.java:4630)
    at java.awt.Container.dispatchEventImpl(Container.java:2099)
    at java.awt.Component.dispatchEvent(Component.java:4460)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
    at java.awt.Container.dispatchEventImpl(Container.java:2085)
    at java.awt.Window.dispatchEventImpl(Window.java:2475)
    at java.awt.Component.dispatchEvent(Component.java:4460)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
    at org.coode.owl.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1198)
    at edu.unika.aifb.rdf.api.syntax.RDFParser.parse(RDFParser.java:112)
    at org.coode.owl.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:86)
    ... 32 more
Caused by: org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
    at org.coode.owl.rdfxml.parser.AbstractTypeAxiomHandler.handleTriple(AbstractTypeAxiomHandler.java:62)
    at org.coode.owl.rdfxml.parser.OWLRDFConsumer.handle(OWLRDFConsumer.java:968)
    at org.coode.owl.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1151)
    ... 34 more


CMD out:
cwd: C:\Programme\Protege_4.0.2
cmd: "C:\Programme\Java\jdk1.6.0_14\bin\java.exe" -Xms209715200 -Xmx209715200 -D
http.proxySet=true -Dhttp.proxyHost=proxy.uni-freiburg.de -Dhttp.proxyPort=80 -c
lasspath "C:\Programme\Protege_4.0.2\org.eclipse.osgi.jar;C:\Programme\Protege_4
.0.2\lax.jar;" com.zerog.lax.LAX "C:/Programme/Protege_4.0.2/Protege.lax" "C:/Do
kumente und Einstellungen/schober/Lokale Einstellungen/Temp/laxC.tmp"
Starting Protege 4 OWL Editor (Version 4.0.115)
Platform:
    Java: JVM 1.6.0_14-b08 Memory: 208M
    Language: de, Country: DE
    Framework: Eclipse (1.5.0)
    OS: WindowsXP (5.1.0)
    Processor: x86
Installed plugin ACE View Tab
Installed plugin DL-Learner Plugin
Installed plugin Annotation Template View
Installed plugin Bookmark View
Installed plugin DL Query Tab
Installed plugin Existential Tree
Installed plugin Browser View (OWLDoc)
Installed plugin OWLViz
Installed plugin owleditor
Installed plugin Protege SKOS plugin
Installed plugin The OWL API
Installed plugin Factplusplus Plug-in
Using OWL API version 2.2.1.1138
Rebuilding entity indices...
... rebuilt in 15 ms
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Programme/Prote
ge_4.0.2/trunk_debugit/src/ontology/dco.owl
No mapping for http://purl.org/biotop/biotop.owl found.
loading http://purl.org/biotop/biotop.owl from http://purl.org/biotop/biotop.owl


-- 

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum    
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711
  
  
          
          
          
          
             
          
          
          

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protege-owl mailing list
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dco.owl (615K) Download Attachment
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Re: owl API backwards incompatible ? Can't open P4.01 owl file after saving it with P4.1beta (new owl API)

Timothy Redmond

As far as I can tell the problem is that P4.01 is not entirely compatible with OWL 2.0.  The purpose of the Protege 4.1 version is to have full compatibility with the OWL 2.0 specification which changed considerably after Protege 4.0.1 was first developed.  The lines that are causing the trouble in question appear to be

    <owl:Axiom>
        <rdfs:comment>axiom annotation example... pipapo</rdfs:comment>
        <owl:annotatedTarget rdf:resource="&dco;HealthCareActivity"/>
        <owl:annotatedSource rdf:resource="&dco;Intervention"/>
        <owl:annotatedProperty rdf:resource="&rdfs;subClassOf"/>
    </owl:Axiom>

As for OWLDoc not working - I did manage to replicate your problem but - strangely - I had OWLDoc working with the latest svn.  I will investigate this a bit.

-Timothy


On 05/31/2010 02:40 AM, Dr. Daniel Schober wrote:
Dear Protege Programmers,

We have recently moved to edit our dco.owl file (attached or see on http://www.imbi.uni-freiburg.de/~schober/dco_owlDoc/dco.owl)  with P.4.1.0 (Alpha, build 102), and have discovered that once saved with P.4.1Alpha it can not be opened by P.4.0.2. anymore, error messages and cmd out, see below. We work on a windows  PC.

Is this a backwards incompatability from the new owl 2 Ver 3 API  to the older owl API as used in P 4.0.2 ? How can I still edit the file in P4.0.2. and also in P4.1 ?
(The main reason we want P 4.1Alpha is that Hermit is so much faster. Maybe this should be made the standard default reasoner for P3.x and P4.0.x as well...The reason we need P4.0.2. is that the OwoDoc plugin does not work in P 4.1.0 ).

Is there a way I can generate an OwlDocHTML serialisation from my owl 2 (P4.1.0 saved) ontology ?

Cheers,
    Daniel Schober.

---

RDFXML Parser Error:
org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.

Stack Trace:
org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
-----------------------------------------------------------------------------------------
org.coode.owl.rdfxml.parser.OWLRDFXMLParserSAXException: org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
    at org.coode.owl.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:90)
    at uk.ac.manchester.cs.owl.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:159)
    at uk.ac.manchester.cs.owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:461)
    at uk.ac.manchester.cs.owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:424)
    at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntology(OWLModelManagerImpl.java:328)
    at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:390)
    at org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:147)
    at org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKit.java:135)
    at org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(ProtegeManager.java:173)
    at org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$5.actionPerformed(ProtegeWelcomeFrame.java:235)
    at org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:97)
    at org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
    at org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:63)
    at java.awt.Component.processMouseEvent(Component.java:6263)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
    at java.awt.Component.processEvent(Component.java:6028)
    at java.awt.Container.processEvent(Container.java:2041)
    at java.awt.Component.dispatchEventImpl(Component.java:4630)
    at java.awt.Container.dispatchEventImpl(Container.java:2099)
    at java.awt.Component.dispatchEvent(Component.java:4460)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
    at java.awt.Container.dispatchEventImpl(Container.java:2085)
    at java.awt.Window.dispatchEventImpl(Window.java:2475)
    at java.awt.Component.dispatchEvent(Component.java:4460)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
    at org.coode.owl.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1198)
    at edu.unika.aifb.rdf.api.syntax.RDFParser.parse(RDFParser.java:112)
    at org.coode.owl.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:86)
    ... 32 more
Caused by: org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing owl:subject triple.
    at org.coode.owl.rdfxml.parser.AbstractTypeAxiomHandler.handleTriple(AbstractTypeAxiomHandler.java:62)
    at org.coode.owl.rdfxml.parser.OWLRDFConsumer.handle(OWLRDFConsumer.java:968)
    at org.coode.owl.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1151)
    ... 34 more


CMD out:
cwd: C:\Programme\Protege_4.0.2
cmd: "C:\Programme\Java\jdk1.6.0_14\bin\java.exe" -Xms209715200 -Xmx209715200 -D
http.proxySet=true -Dhttp.proxyHost=proxy.uni-freiburg.de -Dhttp.proxyPort=80 -c
lasspath "C:\Programme\Protege_4.0.2\org.eclipse.osgi.jar;C:\Programme\Protege_4
.0.2\lax.jar;" com.zerog.lax.LAX "C:/Programme/Protege_4.0.2/Protege.lax" "C:/Do
kumente und Einstellungen/schober/Lokale Einstellungen/Temp/laxC.tmp"
Starting Protege 4 OWL Editor (Version 4.0.115)
Platform:
    Java: JVM 1.6.0_14-b08 Memory: 208M
    Language: de, Country: DE
    Framework: Eclipse (1.5.0)
    OS: WindowsXP (5.1.0)
    Processor: x86
Installed plugin ACE View Tab
Installed plugin DL-Learner Plugin
Installed plugin Annotation Template View
Installed plugin Bookmark View
Installed plugin DL Query Tab
Installed plugin Existential Tree
Installed plugin Browser View (OWLDoc)
Installed plugin OWLViz
Installed plugin owleditor
Installed plugin Protege SKOS plugin
Installed plugin The OWL API
Installed plugin Factplusplus Plug-in
Using OWL API version 2.2.1.1138
Rebuilding entity indices...
... rebuilt in 15 ms
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Programme/Prote
ge_4.0.2/trunk_debugit/src/ontology/dco.owl
No mapping for http://purl.org/biotop/biotop.owl found.
loading http://purl.org/biotop/biotop.owl from http://purl.org/biotop/biotop.owl


-- 

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum    
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711
  
  
          
          
          
          
             
          
          
          
  


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

Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03