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

Tania Tudorache tudorache at stanford.edu
Thu Sep 7 18:27:07 PDT 2006


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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