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[protege-owl] Visualization of ontologies

Dave butlerdi butlerdi at gmail.com
Fri Feb 13 15:18:15 PST 2009


My Bad 34

On Fri, Feb 13, 2009 at 4:25 PM, Nacho Mayorga <nmayorga at gmail.com> wrote:

> 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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> protege-owl at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
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>
>


-- 
Regards

Dave Butler
butlerdi-at-pharm2phork-dot-org

Also on Skype as butlerdi

Get Skype here http://www.skype.com/download.html


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