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[protege-owl] Protege-OWL API, Problem saving an Ontology

Kevin Alonso kalonso at vicomtech.org
Mon Jan 11 02:04:16 PST 2010


Hello Timothy,

I have been doing some tests with other large ontologies and the save 
process goes well. Debugging my program I see nothing rare, it goes well 
only very slow when the program enters in protegeowl-api sources. I have 
tried the saving the ontology in an old 3.4 beta version(build 130) and 
the saving process is very quick. I enclose my protege project if you 
want to test with it.

Could be this a bug of the new releases?


Thank you,

Kevin.

Timothy Redmond escribió:
> No this is very small.  The thesaurus, a moderately large ontology, is
> over 89M.  The size is only one of many metrics of course but I suspect
> that this is not the issue.
> 
> Another thing occurred to me - probably not it - is that maybe your
> process needs more memory (change the -Xmx jvm parameter).  But I think
> that this is unlikely also because things are small.  What I think we
> need to see is some thread dumps.
> 
> -Timothy
> 
> 
> On Thu, 2010-01-07 at 16:19 +0100, Kevin Alonso wrote:
>> Yes, indeed I have add much more information. The ontology I get after 
>> waiting 30 minutes has 1.7MB of information. I have opened the ontology 
>> with Protege 3.4.2 and it goes well but after make some changes and push 
>> the save button the saving process takes 30 minutes too.
>>
>> Is this ontology too much heavy to manage with Protege?
>>
>> Thank you,
>>
>> Kevin.
>>
>> Timothy Redmond escribió:
>>> Kevin Alonso wrote:
>>>> Dear all,
>>>>
>>>> I´m using Protege-OWL API and when i´m going to save the ontology the 
>>>> process takes about 30 minutes. Is it normal?
>>> I have more information but it really is just a confirmation of what I 
>>> said before.  I wrote a small program with the elements that you 
>>> described.  It opened a pizza ontology, added 5000 individuals and saved 
>>> the ontology in 8 seconds.  I loaded the resulting project back into 
>>> protege to check that I had succeeded.
>>>
>>> It is possible that generating a thread dump [1] would help diagnose the 
>>> issue.  Is the process using 100% of the cpu?  A possibility is that 
>>> java is hung or waiting and the save completed or failed.  It is also 
>>> possible that you are generating much more data than I did.  I just 
>>> created 5000 individuals and found that this was a very small amount of 
>>> data.  But you might have added much more information to your individuals.
>>>
>>> -Timothy
>>>
>>> [1] http://java.sun.com/developer/technicalArticles/Programming/Stacktrace/
>>>
>>>
>>>> The code I used:
>>>>
>>>> OWLModel owlModel = null;
>>>> try {
>>>>     owlModel = ProtegeOWL.createJenaOWLModelFromURI(phuri);
>>>> } catch (OntologyLoadException e) {
>>>>     // TODO Auto-generated catch block
>>>>     e.printStackTrace();
>>>>     System.out.println("Errror Loading Ontology: "+ phuri);
>>>> }
>>>>
>>>>
>>>> Then I use a Protege-OWL Java cede classes to create a factory and add 
>>>> some individuals to the ontology.
>>>>
>>>> Factory model = new Factory(owlModel);
>>>> ...
>>>>
>>>>
>>>> And finally I save the ontology:
>>>> JenaOWLModel jenaModel =(JenaOWLModel)owlModel;
>>>> try {
>>>>     jenaModel.save(new File("ModifiedOntology.owl").toURI());
>>>> } catch (Exception e) {
>>>>     // TODO Auto-generated catch block
>>>>     e.printStackTrace();
>>>>     System.out.println("Error saving Ontology");
>>>> }
>>>> System.out.println("Done.");
>>>>
>>>> Is another way to save the ontology more efficiently?
>>>>
>>>>
>>>> Thanks in advance,
>>>>
>>>> Kevin.
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