Protege crashes

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Protege crashes

Carl Hakenäs
Hi,

After 2 hours of building a structure Protoge crashed, all my work is gone.

Maybe have autosave?

This is the log:

------------------------------- Running Reasoner ------------------------------- 
 
An error occurred during reasoning: Literal "The standard mobile architecutre."^^<http://www.w3.org/2001/XMLSchema#language> is malformed. 
org.semanticweb.HermiT.datatypes.MalformedLiteralException: Literal "The standard mobile architecutre."^^<http://www.w3.org/2001/XMLSchema#language> is malformed
at org.semanticweb.HermiT.datatypes.rdfplainliteral.RDFPlainLiteralDatatypeHandler.parseLiteral(RDFPlainLiteralDatatypeHandler.java:101) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.flush(Reasoner.java:426) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:423) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:382) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
An error occurred whilst rendering a token. Token: Enterprise; Token start index: 0 
java.lang.NullPointerException: null
at org.semanticweb.HermiT.Reasoner.getTableau(Reasoner.java:1979) ~[na:na]
at org.semanticweb.HermiT.Reasoner.isConsistent(Reasoner.java:719) ~[na:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.lambda$renderToken$17(OWLCellRenderer.java:789) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer$$Lambda$118/1290921020.run(Unknown Source) ~[na:na]
at org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:118) ~[protege-editor-owl.jar:na]
at org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:182) ~[protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.renderToken(OWLCellRenderer.java:786) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.highlightText(OWLCellRenderer.java:743) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareTextPane(OWLCellRenderer.java:715) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareRenderer(OWLCellRenderer.java:483) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.getTreeCellRendererComponent(OWLCellRenderer.java:369) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.tree.OWLObjectTreeCellRenderer.getTreeCellRendererComponent(OWLObjectTreeCellRenderer.java:34) [protege-editor-owl.jar:na]
at javax.swing.plaf.basic.BasicTreeUI.paintRow(BasicTreeUI.java:1536) [na:1.8.0_40]
at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1224) [na:1.8.0_40]
at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161) [na:1.8.0_40]
at javax.swing.JComponent.paintComponent(JComponent.java:780) [na:1.8.0_40]
at org.protege.editor.owl.ui.tree.OWLObjectTree.paintComponent(OWLObjectTree.java:715) [protege-editor-owl.jar:na]
at javax.swing.JComponent.paint(JComponent.java:1056) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JViewport.paint(JViewport.java:728) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1047) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1047) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5219) [na:1.8.0_40]
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1572) [na:1.8.0_40]
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1495) [na:1.8.0_40]
at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:306) [na:1.8.0_40]
at javax.swing.RepaintManager.paint(RepaintManager.java:1265) [na:1.8.0_40]
at javax.swing.JComponent._paintImmediately(JComponent.java:5167) [na:1.8.0_40]
at javax.swing.JComponent.paintImmediately(JComponent.java:4978) [na:1.8.0_40]
at javax.swing.RepaintManager$4.run(RepaintManager.java:824) [na:1.8.0_40]
at javax.swing.RepaintManager$4.run(RepaintManager.java:807) [na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) [na:1.8.0_40]
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:807) [na:1.8.0_40]
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:782) [na:1.8.0_40]
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:731) [na:1.8.0_40]
at javax.swing.RepaintManager.access$1300(RepaintManager.java:64) [na:1.8.0_40]
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1720) [na:1.8.0_40]
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) [na:1.8.0_40]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:749) [na:1.8.0_40]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_40]
at java.awt.EventQueue$3.run(EventQueue.java:702) [na:1.8.0_40]
at java.awt.EventQueue$3.run(EventQueue.java:696) [na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) [na:1.8.0_40]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:719) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]

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Re: Protege crashes

Rafael Gonçalves
Hi Carl,

Sorry to say that there is no built-in auto-save in Protégé.

There was a malformed literal in the ontology, which HermiT doesn’t forgive. However, I would expect that that alone shouldn’t have caused the workspace to crash. Were there other details in the Protege log?

Cheers,
Rafael

On Aug 2, 2016, at 16:51, Carl Hakenäs <[hidden email]> wrote:

Hi,

After 2 hours of building a structure Protoge crashed, all my work is gone.

Maybe have autosave?

This is the log:

------------------------------- Running Reasoner ------------------------------- 
 
An error occurred during reasoning: Literal "The standard mobile architecutre."^^<http://www.w3.org/2001/XMLSchema#language> is malformed. 
org.semanticweb.HermiT.datatypes.MalformedLiteralException: Literal "The standard mobile architecutre."^^<http://www.w3.org/2001/XMLSchema#language> is malformed
at org.semanticweb.HermiT.datatypes.rdfplainliteral.RDFPlainLiteralDatatypeHandler.parseLiteral(RDFPlainLiteralDatatypeHandler.java:101) ~[na:na]
at org.semanticweb.HermiT.datatypes.DatatypeRegistry.parseLiteral(DatatypeRegistry.java:105) ~[na:na]
at org.semanticweb.HermiT.model.Constant.create(Constant.java:111) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$DataRangeConverter.visit(OWLClausification.java:880) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplNoCompression.accept(OWLLiteralImplNoCompression.java:241) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification$FactClausifier.visit(OWLClausification.java:959) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:119) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.clausify(OWLClausification.java:250) ~[na:na]
at org.semanticweb.HermiT.structural.OWLClausification.preprocessAndClausify(OWLClausification.java:165) ~[na:na]
at org.semanticweb.HermiT.Reasoner.loadOntology(Reasoner.java:208) ~[na:na]
at org.semanticweb.HermiT.Reasoner.flush(Reasoner.java:426) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.ensureRunningReasonerInitialized(OWLReasonerManagerImpl.java:423) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:382) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
An error occurred whilst rendering a token. Token: Enterprise; Token start index: 0 
java.lang.NullPointerException: null
at org.semanticweb.HermiT.Reasoner.getTableau(Reasoner.java:1979) ~[na:na]
at org.semanticweb.HermiT.Reasoner.isConsistent(Reasoner.java:719) ~[na:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.lambda$renderToken$17(OWLCellRenderer.java:789) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer$$Lambda$118/1290921020.run(Unknown Source) ~[na:na]
at org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:118) ~[protege-editor-owl.jar:na]
at org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:182) ~[protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.renderToken(OWLCellRenderer.java:786) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.highlightText(OWLCellRenderer.java:743) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareTextPane(OWLCellRenderer.java:715) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareRenderer(OWLCellRenderer.java:483) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.renderer.OWLCellRenderer.getTreeCellRendererComponent(OWLCellRenderer.java:369) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.tree.OWLObjectTreeCellRenderer.getTreeCellRendererComponent(OWLObjectTreeCellRenderer.java:34) [protege-editor-owl.jar:na]
at javax.swing.plaf.basic.BasicTreeUI.paintRow(BasicTreeUI.java:1536) [na:1.8.0_40]
at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1224) [na:1.8.0_40]
at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161) [na:1.8.0_40]
at javax.swing.JComponent.paintComponent(JComponent.java:780) [na:1.8.0_40]
at org.protege.editor.owl.ui.tree.OWLObjectTree.paintComponent(OWLObjectTree.java:715) [protege-editor-owl.jar:na]
at javax.swing.JComponent.paint(JComponent.java:1056) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JViewport.paint(JViewport.java:728) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1047) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1047) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) [na:1.8.0_40]
at javax.swing.JComponent.paintChildren(JComponent.java:889) [na:1.8.0_40]
at javax.swing.JComponent.paint(JComponent.java:1065) [na:1.8.0_40]
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5219) [na:1.8.0_40]
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1572) [na:1.8.0_40]
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1495) [na:1.8.0_40]
at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:306) [na:1.8.0_40]
at javax.swing.RepaintManager.paint(RepaintManager.java:1265) [na:1.8.0_40]
at javax.swing.JComponent._paintImmediately(JComponent.java:5167) [na:1.8.0_40]
at javax.swing.JComponent.paintImmediately(JComponent.java:4978) [na:1.8.0_40]
at javax.swing.RepaintManager$4.run(RepaintManager.java:824) [na:1.8.0_40]
at javax.swing.RepaintManager$4.run(RepaintManager.java:807) [na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) [na:1.8.0_40]
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:807) [na:1.8.0_40]
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:782) [na:1.8.0_40]
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:731) [na:1.8.0_40]
at javax.swing.RepaintManager.access$1300(RepaintManager.java:64) [na:1.8.0_40]
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1720) [na:1.8.0_40]
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) [na:1.8.0_40]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:749) [na:1.8.0_40]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_40]
at java.awt.EventQueue$3.run(EventQueue.java:702) [na:1.8.0_40]
at java.awt.EventQueue$3.run(EventQueue.java:696) [na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) [na:1.8.0_40]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:719) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]
_______________________________________________
protege-user mailing list
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_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user