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

Timothy Redmond tredmond at stanford.edu
Thu Jan 7 09:40:17 PST 2010


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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> > 
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