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[protege-discussion] Exporting from Protege Database to OWL

Tania Tudorache tudorache at stanford.edu
Thu May 1 16:52:37 PDT 2008


Cecil,

Thank you very much for sending the SQL dump.

I've debugged this and the "problem" is that the Concept metaclass is a 
subclass of :CLASS rather than of :STANDARD-CLASS. In most ontologies, 
the metaclasses are subclasses of the latter. The OWL converter did not 
know how to interpret the non-standard meta-class, so it did not convert 
it. As a consequence, the classes of that metaclass where also frames 
classes, not OWL Named Classes, as expected by the converter.

The fix is simple. Just move the Concept metaclass under :STANDARD-CLASS 
and the conversion to OWL will work fine.

If you will use metaclasses for frames ontologies in future, I recommend 
to make them a subclass of :STANDARD-CLASS, rather than of :CLASS.

Tania


Cecil O. Lynch, MD, MS wrote:
> Tania,
>
> BTW, I just tried using 3.4 build 130 both with and without the native
> writer checked and failed on both. You should have the files now. Let me
> know if the zip file did not make it through the firewalls and I will rename
> and resend.
>
> thanks
>
> Cecil
>
> -----Original Message-----
> From: protege-discussion-bounces at mailman.stanford.edu
> [mailto:protege-discussion-bounces at mailman.stanford.edu] On Behalf Of Tania
> Tudorache
> Sent: Wednesday, April 30, 2008 5:24 PM
> To: User support for Core Protege and the Protege-Frames editor
> Subject: Re: [protege-discussion] Exporting from Protege Database to OWL
>
> Hi Cecil,
>
> I assume you tried File -> Export to Format -> OWL. Did you try to 
> enable the chechbox "Use Protege native writer"?
>
> I have just tried now to export a project from Frames DB to an OWL file 
> and I did not reproduce the exception.
>
> Can you send me privately a dump of the ontology that caused this behavior?
>
> Tania
>
>
> Cecil O. Lynch, MD, MS wrote:
>   
>> Tania,
>>
>> I am trying to export a very simple (but moderate size) Protégé 
>> database file to OWL and get the following trace:
>>
>> cwd: C:\Program Files\Protege_3.3.1\
>> cmd: "C:\Program Files\Protege_3.3.1\jre\bin\java.exe" -Xms1215098112 
>> -Xmx121509
>> 8112 -classpath "C:\Program Files\Protege_3.3.1\protege.jar;C:\Program 
>> Files\Pro
>> tege_3.3.1\looks-2.1.3.jar;C:\Program 
>> Files\Protege_3.3.1\unicode_panel.jar;C:\P
>> rogram Files\Protege_3.3.1\driver.jar;C:\Program 
>> Files\Protege_3.3.1\dbdrivers\m
>> ysql-connector-java-5.1.6-bin.jar;C:\Program 
>> Files\Protege_3.3.1\driver1.jar;C:\
>> Program Files\Protege_3.3.1\driver2.jar;C:\Program 
>> Files\Protege_3.3.1\plugins\e
>> du.stanford.smi.protegex.changes\change-model.jar;C:\Program 
>> Files\Protege_3.3.1
>> \lax.jar;" com.zerog.lax.LAX "C:/Program 
>> Files/Protege_3.3.1/Protege.lax" "C:/Do
>> cuments and Settings/Cecil/Local Settings/Temp/lax98.tmp"
>> CONFIG: Protege 3.3.1 Build 430, JVM 1.5.0_11-b03, memory=1207M, 
>> Windows XP, enc
>> oding=UTF-8, language=en, country=US
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
>> CONFIG: Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
>> CONFIG: Loaded plugin com.ngs - ONTOBaseTab
>> WARNING: java.lang.NoClassDefFoundError: 
>> edu/stanford/smi/protege/widget/_Abstra
>> ctWidget -- PluginUtilities.isLoadableClass()
>> WARNING: missing file: doc/index.html -- PluginUtilities.loadURL()
>> CONFIG: Loaded plugin dfki.protege.ontoviz
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.chatPlugin
>> CONFIG: Loaded plugin edu.stanford.smi.protege.collab - Collaborative 
>> Protege
>> CONFIG: Loaded plugin edu.stanford.smi.protege.script - Script Plugin
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.standard_extensions - 
>> Graph Widg
>> et, Table Widget
>> CONFIG: Loaded plugin edu.stanford.smi.protege.stringsearch - String 
>> Search Tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.datamaster - 
>> DataMaster Tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.facets_tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.instance_tree
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
>> CONFIG: Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
>> CONFIG: Loaded plugin images
>> CONFIG: Loaded plugin OntoReason.DataImport.v2
>> CONFIG: Loaded plugin org.algernon - Algernon
>> CONFIG: Loaded plugin org.ecoinformatics.seek.growl.protegex - GrOWL View
>> CONFIG: Loaded plugin plugins
>> CONFIG: Loaded plugin se.liu.ida.JessTab - JessTab Plugin
>> CONFIG: Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.debugger
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owldoc
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlviz
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic 
>> Wizards
>> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL 
>> Wizards
>> INFO: Load time for file:\C:\Program%20Files\Protege_3.3.1\CHT.pprj 
>> <file:%5CC:%5CProgram%20Files%5CProtege_3.3.1%5CCHT.pprj> = 0 sec (pro
>> ject) + 1 sec (ui)
>> [ProtegeUI]  Warning: No ProjectView registered for project CHT
>> [ProtegeUI]  Warning: No ProjectView registered for project CHT
>> SEVERE: Exception caught -- java.lang.ClassCastException: 
>> edu.stanford.smi.prote
>> ge.model.DefaultCls
>>         at 
>> edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel.createOWLNa
>> medClass(Unknown Source)
>>         at 
>> edu.stanford.smi.protegex.owl.storage.ProtegeSaver.createCls(Unknown
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.storage.KnowledgeBaseCopier.getNewCls(U
>> nknown Source)
>>         at 
>> edu.stanford.smi.protegex.owl.storage.ProtegeSaver.getNewCls(Unknown
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.storage.KnowledgeBaseCopier.createClses
>> (Unknown Source)
>>         at 
>> edu.stanford.smi.protegex.owl.storage.KnowledgeBaseCopier.run(Unknown
>>  Source)
>>         at 
>> edu.stanford.smi.protegex.owl.jena.export.JenaExportPlugin.exportProj
>> ect(Unknown Source)
>>         at 
>> edu.stanford.smi.protegex.owl.jena.export.JenaExportPlugin.handleExpo
>> rtRequest(Unknown Source)
>>         at 
>> edu.stanford.smi.protege.ui.ProjectManager.exportProjectRequest(Unkno
>> wn Source)
>>         at 
>> edu.stanford.smi.protege.action.ExportPluginAction.actionPerformed(Un
>> known 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)
>>
>> I am using Protégé 3.3.1 Build 430 on an XP platform
>>
>>     
>
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