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[protege-owl] NCI Thesaurus load problems (NOT MEMORY PROBLEM)

Julia Dmitrieva jdmitrie at liacs.nl
Fri Sep 8 01:13:42 PDT 2006


Thank you, Tania.

I try  to change the repositories for Thesaurus.owl.
But I have still the Out of memory problem.
I have changed the protege.lax file, and I
have now 2G runtime memory. But if I try to
run Protege with more than 1G memory than
Protege starts with empty screen (I have written
about this problem 2 month ago). Thus I can load
the thesaurus only with 0.9G of memory, but if
I try to do something with it than I have my
lovely problem : Exception in thread "AWT-EventQueue-0" 
java.lang.OutOfMemoryError: Java heap spa
ce.
May be can I just change the Thesaurus.owl file with following
In place of:
<owl:imports 
rdf:resource="http://protege.stanford.edu/plugins/owl/protege"/>
have to be:
<owl:imports rdf:resource="file:///C:/Program 
Files/Protege_3.2_beta/plugins/edu.stanford.smi.protegex.owl/protege.owl"/>

In the case of you first solution.
I am using Eclipse and I have added needed jar's to
the class path, I mean Protege.jar and other jar's from
protege/plugins.

I citate from the The Protégé-OWL API - Programmer's Guide:
"If you are using a Java IDE such as Eclipse or IntelliJ, please select 
the Protege installation folder as your project home. Then add all the 
jar files from the installation to your project classpath. Set your 
compiler output path to plugins/classes."
The probelem is that I am not really understand what it means.

Do I have to create my project in Protege folder,
thus everething from Protege needs to be loaded?


Thank you for help,
Julia

Tania Tudorache wrote:
> Julia,
> 
> The problem is that when you run the program that uses the Protege API, 
> it does not find the Protege ontology, which is imported in the NCI 
> thesaurus (the ontology is stored as a file "protege.owl" in the owl 
> plugins directory). In order to solve this problem, you have two solutions:
> 
> 1. You execute the program in the same directory where Protege is installed.
> 
> or
> 
> 2. You edit the repository file of your ontology and add the following 
> line to it:
> 
>     
> file:/C:/MyPath/Protege_3.2_b331/plugins/edu.stanford.smi.protegex.owl/protege.owl?forceReadOnly=true
> 
> You replace the path with the path to the local protege.owl file in the 
> owl plugins directory. You can do this also from the Protege GUI, in the
> "OWL" Menu -> "Ontology repositories" -> "Project repositories" and add 
> there a repository for a local file that points to the protege.owl in 
> the owl plugins directory.
> 
> Tania
> 
> 
> 
> Julia Dmitrieva wrote:
> 
> 
>>Dear Protege list.
>>
>>I get problems with loading of NCI
>>Thesaurus.owl via Protege API.
>>
>>I can load all triples without problems, but after that
>>i get the following error message.
>>Loaded 950000 triples
>>Loaded 955000 triples
>>[ProtegeOWLParser] Importing 
>>http://protege.stanford.edu/plugins/owl/protege (from 
>>http://protege.stanford.edu/plugins/owl/protege [actual ontology at 
>>this location: null])
>>[ProtegeOWLParser] Completed triple loading after 324485 ms
>>[TripleChangePostProcessor] Completed lists after 156 ms
>>[TripleChangePostProcessor] Completed anonymous classes after 656 ms
>>[TripleChangePostProcessor] Completed deprecated classes after 0 ms
>>[TripleChangePostProcessor] Completed properties after 94 ms
>>
>> :-( :-( :-( :-( And that  :-( :-( :-( :-(
>>
>>java.lang.IllegalArgumentException: null slot
>>    at 
>>edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.assertNotNull(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.checkSlot(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.getDirectOwnSlotValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getDirectOwnSlotValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispatch.getDirectOwnSlotValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatchFrameStore.getDirectOwnSlotValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getDirectOwnSlotValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getDirectOwnSlotValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.framestore.OWLFrameStore.getDirectOwnSlotValuesConverting(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.impl.OWLUtil.getPropertyValues(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.impl.OWLUtil.getPropertyValue(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.impl.AbstractRDFSClass.getPropertyValue(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.classdisplay.AbstractOWLClassDisplay.getCommentText(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.classdisplay.AbstractOWLClassDisplay.getDisplayText(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.impl.AbstractOWLAnonymousClass.getBrowserText(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.DuplicateSuperclassesPostProcessor.removeDuplicateSuperclasses(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.DuplicateSuperclassesPostProcessor.<init>(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.TripleChangePostProcessor.postProcess(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStoreModel.endTripleStoreChanges(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown 
>>Source)
>>    at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown 
>>Source)
>>    at 
>>edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(Unknown 
>>Source)
>>    at Thesaurus.thesaurusMining.main(thesaurusMining.java:40)
>>
>>What I find very strange, is that the loading of thesaurus.owl is
>>going OK if I load it from Proptege application.
>>I mean, that it must also be possible to load it via OWL Proptege API.
>>I don't know what I am missing.
>>Do you have some suggestions.
>>
>>Thanks,
>>Julia
>>
>>
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>>
>>
> 
> 
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-- 
Julia Dmitrieva

LIACS Office:  124
Phone:  +31 (0)71 – 5275777
E-Mail:  jdmitrie at liacs.nl

Member of:  Imaging
Scientific Personnel




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