Reproducing Protege reasoning results programmatically in Java

[Maxwell Neal]

Hi all,

I'm trying to use Hermit in Java to programmatically classify an ontology that contains 893 classes, 134 individuals and 4 SWRL rules. Several of the classes contain equivalent class axioms that use Class Expressions. Many of the individuals have Class Expressions as their asserted Types, including closure axioms. 

I can successfully classify the ontology using Protege 4.3 (takes about 1 minute) but I need to classify the ontology programmatically. I've been able to load in the ontology and verify it's consistent using the Hermit API, but I'm struggling to figure out how I can get the Hermit API to generate the inferred axioms that Protege produces.

I've tried adapting the MaterialiseInferrences.java code provided in the Hermit examples directory, but my program seems to get stuck on the fillOntology() call. Is there a way to perform my reasoning task without calling the OWL API? Any other suggestions/pointers on how to perform this classification with the same expediency as Protege?

Many thanks!

-Max

[Ignazio Palmisano]

The example is using multiple inference generators - if you only need
a few of them, you could skip the unnecessary ones.
Or, you could use them one at a time to see which one is taking too
long, and at that point we can look into ways to improve it.
Cheers,
I.

>
> Many thanks!
>
> -Max
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[Maxwell Neal]

Hi Ignazio,

Turns out that it was the InferredDisjointClassesAxiomGenerator that was causing my program to stick. If I comment out the lines that add that Generator, Hermit performs the classification in about the same amount of time as Protege.

I've been able to generate the axioms I need without using the InferredDisjointClassesAxiomGenerator. Thanks!

M

[Sathyamoorthy R]

Hi, could you pleases share any example of that?

[Kenny Cason]

I'm not sure I completely understand this question. Are you trying to generate axioms outside of the HermiT reasoner, using the same calls HermiT is using? If so I don't know why you would want to do that when HermiT will do it for you. Here is a partial example of that. Forgive me if I'm answering the wrong question:

public Boolean createReasoner(OWLOntology ont) {

    Configuration config=new Configuration();
    //Configuration.PrepareReasonerInferences prefs = new Configuration.PrepareReasonerInferences();
    //config.prepareReasonerInferences = prefs;
    //config.freshEntityPolicy = owlAPIConfiguration.getFreshEntityPolicy();
    //config.individualNodeSetPolicy = owlAPIConfiguration.getIndividualNodeSetPolicy();
    //config.individualTaskTimeout = owlAPIConfiguration.getTimeOut();
    config.reasonerProgressMonitor = new HxProgressMonitor();
    config.ignoreUnsupportedDatatypes = false;
    config.throwInconsistentOntologyException = false;

    reasoner = new Reasoner(config, ont);

    // Get a Start date/time
    Date d1 = new Date();

    // Set the config to inference every type available
    Set<InferenceType> precompute = EnumSet.of(InferenceType.CLASS_HIERARCHY);
    precompute.addAll(reasoner.getPrecomputableInferenceTypes());

    // Do the actual inferencing
    reasoner.precomputeInferences(precompute.toArray(new InferenceType[precompute.size()]));

    //Get a Stop date/time
    Date d2 = new Date();

    // Compute the execution time
    DecimalFormat myDecimalFormatter = new DecimalFormat("###,###.###");
    System.out.println("HxReasoner.precompute: inference execution time: " +
            myDecimalFormatter.format((((double) d2.getTime() - d1.getTime()) / 1000) / 60) +
            " minutes");
}

[Sathyamoorthy R]

I assumed the question matches my requirement

- Sathya