Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Julia Dmitrieva jdmitrie at liacs.nl
Fri Sep 8 02:31:23 PDT 2006


Hello Tania,

After the changing of Thesaurus.owl file with the
good
<owl:imports 
rdf:resource="file:///C:/Program%20Files/Protege_3.2_beta/plugins/edu.stanford.smi.protegex.owl/protege.owl"/>
I can load it in my java Project.

May be have you some suggestions about why Protege cames with empty UI
when I try to start it with runtime memory above 1G.

Thank you,
Julia

Julia Dmitrieva wrote:
> 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
>>>
>>>
>>>-------------------------------------------------------------------------
>>>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>>>
>>>
>>
>>
>>_______________________________________________
>>protege-owl mailing list
>>protege-owl at lists.stanford.edu
>>https://mailman.stanford.edu/mailman/listinfo/protege-owl
> 
> 
> 


-- 
Julia Dmitrieva

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

Member of:  Imaging
Scientific Personnel




More information about the protege-owl mailing list