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I am running Pellet with Jena as the following:

public void storeInferredModel(Data data) {
    System.out.println("creating inferred dataset ");
    Dataset dataset = TDBFactory.createDataset(data.getInferredResultsPath());
    System.out.println("creating OntModel ");
    OntModel Infmodel = ModelFactory.createOntologyModel(
                          PelletReasonerFactory.THE_SPEC, 
                          dataset.getNamedModel(this.URL));
    System.out.println("adding schema (OWL) to OntModel");
    Infmodel.add(this.owl);
    System.out.println("adding data (RDF) to OntModel ");
    Infmodel.add(data.tdb);
    System.out.println("creating ModelExtractor ");
    ModelExtractor ext = new ModelExtractor(Infmodel);
    System.out.println("replacing OntModel by the Extracted Model");
    dataset.replaceNamedModel(this.URL, ext.extractModel());
    System.out.println("saving inferred model");
    Infmodel.close();
    System.out.println("closing inferred dataset");
    dataset.close();
}

My TDB or the raw data is 2.7G. I have been running the reasoner against the TDB but I got the problem of “GC overhead limit exceeded java” though I give the program around 45G memory and the reasoner has taken only 30G and then crashed. In other words, it did not reached the Max of computer memory.

Another question is with Pellet, when I run the code above in small dataset I got too many sameAS, disjoint, etc. Is that a bug or am I doing something wrong with Pellet?

Joshua Taylor
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Dr.AdeeB
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    What do you mean by “too many sameAs, disjoint, etc.”? It's possible, though unlikely, that there's a bug with Pellet. It's also possible, and in my experience, more likely that there's a bug in the data. It would probably be better to document what unexpected results you're getting from Pellet, reproduce them in a minimal working example, and ask a separate question about that. – Joshua Taylor Jul 17 '13 at 01:34
  • thanks Joshua. I do not think there is a problem with the TDB as it works with SPARQL update for example. I email Pellet people and no one has answer my question and in fact the form has been sleepy for more the a month. The confusing this is that it works with small dataset and produces the results but not with the big one. Also, when I run Pellet APi with small dataset , I do still get these smaeAs, disjoint things for every single resource in my data. – Dr.AdeeB Jul 17 '13 at 06:51
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    You'll need to show a minimal example of the unexpected behavior that you're getting from Pellet in order for anyone on StackOverflow to help. I will note that Pellet computes the full logical closure, so you do end up with a bunch of trivially true results like `x owl:sameAs x`, or `someClass owl:disjointWith owl:Nothing`, and `someProperty owl:propertyDisjointWith owl:BottomObjectProperty`, and the like. Typically you ignore those sorts of things by using an appropriate ModelExtractor. Without a minimal working example of the behaviors you're getting, though, we can't be of much more help. – Joshua Taylor Jul 17 '13 at 11:30
  • ALright Joshua , I will do such a thing. Where should I post it ? – Dr.AdeeB Jul 17 '13 at 20:50
  • If I were you, I'd post it as an another Stack Overflow question, and post a link to it here in a comment. – Joshua Taylor Jul 17 '13 at 21:07

0 Answers0