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[protege-discussion] Exporting from Protege Database to OWL

Cecil O. Lynch, MD, MS clynch at surewest.net
Wed Apr 30 15:11:26 PDT 2008


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 = 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 

-----Original Message-----
From: protege-discussion-bounces at mailman.stanford.edu
[mailto:protege-discussion-bounces at mailman.stanford.edu] On Behalf Of
tudorache at stanford.edu
Sent: Wednesday, April 30, 2008 1:26 PM
To: protege-discussion at mailman.stanford.edu
Subject: [protege-discussion] Tania Tudorache <tudorache at stanford.edu>: Re:
Editing UNSPSC with protege frames

Dies ist eine Benachrichtigung des E-Mail-Servers von faktorM. · Mensch im
Unternehmen.

Folgende E-Mail ist eingetroffen:

  Absender:     Tania Tudorache <tudorache at stanford.edu>
  Betreff:      Re: [protege-discussion] Editing UNSPSC with protege
                frames
  Organisation: Biomedical Informatics Research
  Empfänger:    protege-discussion at mailman.stanford.edu
  Kopieliste:   [keine Angabe]
  Gesendet:     Mittwoch, 30. April 2008, 13:13:01 Uhr -0700
  Anhang:       "empty_RDF.rdf"

clamav didn't found any malware; Gefährlicher Anhang gefunden:
"empty_RDF.rdf"; Dateityp: rdf-Datei. Dieser Dateityp wird von den
Sicherheitsrichtlinien nicht zugelassen. Die Datei wird ausgeblendet. Bitte
wenden Sie sich innerhalb der nächsten 90 Tage an Ihren Administrator, falls
Sie sie benötigen! (mailto:administrator at faktorm.de)

Vollständiger Nachrichtentext in reduzierter Formatierung:

Antonia,

There are two ways of editing RDF(S) files in protege:

1. Solution 1 is  to use the RDF Backend (the UI similar to Protege 
frames). Then, you need indeed two files: the schema (rdfs) and the 
instances file (rdf). However, the distinction about schema and 
instances is not a strict one. So, you can just create an empty rdf file 
(with the same name as the rdfs file, but with extension ".rdf"). You 
can use the file attached to this email and rename it. Start protege, 
click on New project, select "RDF Files" in the "Select Project Type" 
and enable the checkbox "Create from existing sources". Then follow the 
wizard steps.

2. Solution 2 is to use the Protege-OWL RDF backend (the UI will look 
like the Protege-OWL one). For this, you can use only one file (no need 
for the rdf file). Start Protege, "Create New project", select "OWL/RDFS 
files" and click "Create from existing sources" and in the next screen, 
add the rdfs file in the Ontology URI field.

I hope this helps.

Tania

Antonia Iliopoulou wrote:
> Hi everyone,
>  
> I would like to ask if there is anybody that has edited the unspsc 
> library with the protege frames.
> My problem is that in order to impoted it to the protege I need an 
> rdfs file (to describe the schema) and an rdf file (to describe the 
> instances). But I have only an rdfs file wich describes the instances 
> as classes. The solution I have thought is to transform this file into 
> 2 files (rdfs + rdf). But this procedure is time consuming as the file 
> is almost 4MB! Could you please give me an idea about what to do?
> Or if there is anyone who has already worked with this library could 
> he give me any clue?
>  
> Thank you in advance,
>  
> Best Regards,
> Antonia
>  
> ------------------------------------------------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
http://protege.stanford.edu/doc/faq.html#01a.03 
>   


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No virus found in this incoming message.
Checked by AVG. 
Version: 7.5.524 / Virus Database: 269.23.6/1404 - Release Date: 4/29/2008
6:27 PM
 

No virus found in this outgoing message.
Checked by AVG. 
Version: 7.5.524 / Virus Database: 269.23.6/1404 - Release Date: 4/29/2008
6:27 PM
 
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