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[protege-owl] Visualization of ontologies

Nacho Mayorga nmayorga at gmail.com
Fri Feb 13 07:25:50 PST 2009


Hi Dave,

I'm sorry, but I haven't actually understood your sentence (my brain must be
on stand-by today). What is 3.14 (besides PI :-D)?

From: Dave butlerdi <butlerdi at gmail.com>
> To: User support for the Protege-OWL editor <
> protege-owl at lists.stanford.edu>
> Date: Fri, 13 Feb 2009 11:23:51 +0100
> Subject: Re: [protege-owl] Visualization of ontologies
> 3.14, just got in and brain is not functioning yet ...
>
> On Fri, Feb 13, 2009 at 11:23 AM, Dave butlerdi <butlerdi at gmail.com>wrote:
>
>> If I get some time I will install as I have wanted to for a while now.
>> What version of Protege are you using ?.
>> Also try a few different Ontologies and see if the result is the same. I
>> find quite often that there is something in one or the other that freaks
>> tools out.
>>
>
Good idea. I've tried to load the pizza ontology and a number of other small
ontologies availables on the web (but previously saved onto my disk), both
in owl and rdf formats. The results have been always similar. At the end of
this message, I'm copying three examples, adding the ontology names and
their URIs before the stack trace resulting from enabling ontosphere on each
of them.

BTW, I've sent a message through SourceForge to the plugin's author as the
ontosphere3d-users list does not look like it's active...

Cheers,

              Nacho

P.S. Find below thw traces for three small ontologies. Notice that, on the
two last cases, it looks like it's the initialize method what actully causes
the exception to be thrown.

   - autos (URI=http://www.owl-ontologies.com/autos.owl)
      - Loading triples from:
      file:/home/nmayorga/tinuviel/Work/semweb/ontologies/topic/autos.owl
      Completed triple loading after 1049 ms
      Postprocess: Process entities with incorrect Java type (0 entities)
      ... 0 ms
      Postprocess: Process metaclasses (3 metaclasses) ... 0 ms
      Postprocess: Process subclasses of rdf:List (1 classes) ... 1 ms
      Postprocess: Instances with multiple types (128 instances) ... 30 ms
      Postprocess: Add inferred superclasses ... 0 ms
      Postprocess: Process orphan classes (90 classes) ... 6 ms
      Postprocess: Generalized Concept Inclusion (0 axioms) ... 1 ms
      Postprocess: Abstract classes... 0 ms
      Postprocess: Domain and range of properties... 17 ms
      Postprocess: Possibly typed entities (0 resources) ... 0 ms
      Updating underlying frames model in 0 ms
      Protege Wizards v1.0 beta build 15
      Loaded OWL wizards library
      UI display time = 3 sec
      SEVERE: Uncaught Exception -- java.lang.NoClassDefFoundError:
      javax/vecmath/Color3f
          at
      it.polito.elite.visualization.ontoviewer.userInterfaces.VisualizationOptions.<clinit>(VisualizationOptions.java:43)
          at
      it.polito.elite.protege.plugin.OntoSpherePlugin.initialize(OntoSpherePlugin.java:77)
          at
      edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
          at edu.stanford.smi.protege.ui.ProjectView.addEnabledTabs(Unknown
      Source)
          at
      edu.stanford.smi.protege.ui.ProjectView.synchronizeTabbedPane(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.reloadPartial(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.reload(Unknown Source)
          at edu.stanford.smi.protege.ui.ProjectManager.reloadUI(Unknown
      Source)
          at
      edu.stanford.smi.protege.ui.ProjectManager.configureProjectRequest(Unknown
      Source)
          at
      edu.stanford.smi.protege.action.ConfigureProject.actionPerformed(Unknown
      Source)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
      Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
      Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.AbstractButton.doClick(Unknown Source)
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
          at
      javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
      Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown
      Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown
      Source)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
      Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.run(Unknown Source)


   -  beer (URI=http://purl.org/net/ontology/beer.owl)
      - Loading triples from:
      file:/home/nmayorga/tinuviel/Work/semweb/ontologies/topic/beer.owl
          Completed triple loading after 37 ms
      Postprocess: Process entities with incorrect Java type (2 entities)
      ... 0 ms
      Postprocess: Process metaclasses (3 metaclasses) ... 0 ms
      Postprocess: Process subclasses of rdf:List (1 classes) ... 0 ms
      Postprocess: Instances with multiple types (10 instances) ... 0 ms
      Postprocess: Add inferred superclasses ... 0 ms
      Postprocess: Process orphan classes (61 classes) ... 1 ms
      Postprocess: Generalized Concept Inclusion (0 axioms) ... 0 ms
      Postprocess: Abstract classes... 0 ms
      Postprocess: Domain and range of properties... 3 ms
      Postprocess: Possibly typed entities (13 resources) ... 0 ms
      Updating underlying frames model in 0 ms
      Protege Wizards v1.0 beta build 15
      Loaded OWL wizards library
      UI display time = 0 sec
      SEVERE: Uncaught Exception -- java.lang.NoClassDefFoundError
          at
      it.polito.elite.protege.plugin.OntoSpherePlugin.initialize(OntoSpherePlugin.java:77)
          at
      edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
          at edu.stanford.smi.protege.ui.ProjectView.addEnabledTabs(Unknown
      Source)
          at
      edu.stanford.smi.protege.ui.ProjectView.synchronizeTabbedPane(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.reloadPartial(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.reload(Unknown Source)
          at edu.stanford.smi.protege.ui.ProjectManager.reloadUI(Unknown
      Source)
          at
      edu.stanford.smi.protege.ui.ProjectManager.configureProjectRequest(Unknown
      Source)
          at
      edu.stanford.smi.protege.action.ConfigureProject.actionPerformed(Unknown
      Source)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
      Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
      Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.AbstractButton.doClick(Unknown Source)
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
          at
      javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
      Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown
      Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown
      Source)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
      Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.run(Unknown Source)
   - travel (URI=http://www.owl-ontologies.com/travel.owl)
      - Loading triples from:
      file:/home/nmayorga/tinuviel/Work/semweb/ontologies/topic/travel.owl
          Completed triple loading after 34 ms
      Postprocess: Process entities with incorrect Java type (0 entities)
      ... 0 ms
      Postprocess: Process metaclasses (3 metaclasses) ... 0 ms
      Postprocess: Process subclasses of rdf:List (1 classes) ... 0 ms
      Postprocess: Instances with multiple types (23 instances) ... 1 ms
      Postprocess: Add inferred superclasses ... 1 ms
      Postprocess: Process orphan classes (34 classes) ... 1 ms
      Postprocess: Generalized Concept Inclusion (0 axioms) ... 0 ms
      Postprocess: Abstract classes... 0 ms
      Postprocess: Domain and range of properties... 1 ms
      Postprocess: Possibly typed entities (0 resources) ... 0 ms
      Updating underlying frames model in 0 ms
      Protege Wizards v1.0 beta build 15
      Loaded OWL wizards library
      UI display time = 0 sec
      SEVERE: Uncaught Exception -- java.lang.NoClassDefFoundError
          at
      it.polito.elite.protege.plugin.OntoSpherePlugin.initialize(OntoSpherePlugin.java:77)
          at
      edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
          at edu.stanford.smi.protege.ui.ProjectView.addEnabledTabs(Unknown
      Source)
          at
      edu.stanford.smi.protege.ui.ProjectView.synchronizeTabbedPane(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.reloadPartial(Unknown
      Source)
          at edu.stanford.smi.protege.ui.ProjectView.reload(Unknown Source)
          at edu.stanford.smi.protege.ui.ProjectManager.reloadUI(Unknown
      Source)
          at
      edu.stanford.smi.protege.ui.ProjectManager.configureProjectRequest(Unknown
      Source)
          at
      edu.stanford.smi.protege.action.ConfigureProject.actionPerformed(Unknown
      Source)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
      Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
      Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.AbstractButton.doClick(Unknown Source)
          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
          at
      javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
      Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown
      Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown
      Source)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
      Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.run(Unknown Source)

-- 
Nacho Mayorga
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