javaowlowl-apin-triples

Can't save the ontology with NTriples (OWLAPI)

I tried to save my ontology as NTriples format using owlapi. This error appear when I try to save my ontology:

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 1
    at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
    at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
    at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
    at java.base/java.util.Objects.checkIndex(Objects.java:373)
    at java.base/java.util.ArrayList.get(ArrayList.java:426)
    at java.base/java.util.Collections$UnmodifiableList.get(Collections.java:1321)
    at java.base/java.util.Collections$UnmodifiableList.get(Collections.java:1321)
    at org.semanticweb.owlapi.rdf.model.AbstractTranslator.lambda$visit$3(AbstractTranslator.java:710)
    at java.base/java.lang.Iterable.forEach(Iterable.java:75)
    at org.semanticweb.owlapi.rdf.model.AbstractTranslator.visit(AbstractTranslator.java:709)
    at org.semanticweb.owlapi.model.OWLSameIndividualAxiom.accept(OWLSameIndividualAxiom.java:51)
    at org.semanticweb.owlapi.rdf.model.AbstractTranslator.translate(AbstractTranslator.java:288)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
    at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1624)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
    at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.createGraph(RDFRendererBase.java:484)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.createGraph(RDFRendererBase.java:471)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.lambda$renderEntities$5(RDFRendererBase.java:294)
    at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:176)
    at java.base/java.util.ArrayList$Itr.forEachRemaining(ArrayList.java:1002)
    at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
    at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.renderEntities(RDFRendererBase.java:295)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.renderInOntologySignatureEntities(RDFRendererBase.java:280)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.renderOntologyComponents(RDFRendererBase.java:263)
    at org.semanticweb.owlapi.rdf.RDFRendererBase.render(RDFRendererBase.java:258)
    at org.semanticweb.owlapi.rio.RioStorer.storeOntology(RioStorer.java:230)
    at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:85)
    at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:72)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1324)
    at preprocess.PositiveInference.inferringSemanticsofEquality(PositiveInference.java:117)
    at preprocess.PositiveInference.inferencing(PositiveInference.java:85)
    at preprocess.PositiveInference.main(PositiveInference.java:65)

And the code that referenced in error is:

NTriplesDocumentFormat nTriplesFormat = new NTriplesDocumentFormat();

try {
        ontologyManager.saveOntology(ontologyInferred, nTriplesFormat, IRI.create(file.toURI()));
} catch (OWLOntologyStorageException e) {
        e.printStackTrace();
}

The ontology:

SameIndividual(<http://www.example.com/individual/eq#PB> )
SameIndividual(<http://www.example.com/individual/eq#transY> )
SameIndividual(<http://www.example.com/individual/eq#symX> )
SameIndividual(<http://www.example.com/individual/eq#OC> )
SameIndividual(<http://www.example.com/individual/eq#transZ> )
SameIndividual(<http://www.example.com/individual/eq#SAA> )
SameIndividual(<http://www.example.com/individual/eq#transX> )
SameIndividual(<http://www.example.com/individual/eq#OAC> )
SameIndividual(<http://www.example.com/individual/eq#refO> )
SameIndividual(<http://www.example.com/individual/eq#refS> )
SameIndividual(<http://www.example.com/individual/eq#SA> )
SameIndividual(<http://www.example.com/individual/eq#PAB> )
SameIndividual(<http://www.example.com/individual/eq#transX> <http://www.example.com/individual/eq#transY> <http://www.example.com/individual/eq#transZ> )
SameIndividual(<http://www.example.com/individual/eq#symY> )

The reflexsive sameAs axiom result of inferrencing based on OWL 2 RL/RDF rules eq-ref

If: T(?s, ?p, ?o) then: T(?s, owl:sameAs, ?s)

SameIndividual(http://www.example.com/individual/eq#PB )

The inferencing code:

result.add(dataFactory.getOWLSameIndividualAxiom(individual, individual));

I can save my ontology as OWLXMLFormat, but since I am building a dataset that need in triple form. Is there any solution to save it in any triple form?

Other Format already tried and error:

NTriplesDocumentFormat nTriplesFormat = new NTriplesDocumentFormat();
N3DocumentFormat n3Format = new N3DocumentFormat();
TrigDocumentFormat trigFormat = new TrigDocumentFormat();
TurtleDocumentFormat  turtleFormat = new TurtleDocumentFormat();
RioTurtleDocumentFormat  rioFormat = new RioTurtleDocumentFormat();

Edit:

The full inferrence code:

public class InferredSameIndividualAxiomGenerator extends InferredIndividualAxiomGenerator<OWLSameIndividualAxiom>{
    
    @Override
    protected void addAxioms(OWLNamedIndividual entity, OWLReasoner reasoner, OWLDataFactory dataFactory, Set<OWLSameIndividualAxiom> result) {

        Set<OWLNamedIndividual> sameIndividuals = asUnorderedSet(reasoner.getSameIndividuals(entity).entities());
        sameIndividuals.add(entity);
        result.add(dataFactory.getOWLSameIndividualAxiom(entity, entity));
        if (sameIndividuals.size() > 1) 
            result.add(dataFactory.getOWLSameIndividualAxiom(sameIndividuals));
    }

    @Override
    public String getLabel() {
        return "Same Individuals T(?x, owl:sameAs, ?y)";
    }
}
Solution

  • As a workaround ONT-API could be used.
    Since ONTAPI is a RDF-centric OWLAPI implementation, there must be no problem with any RDF-serialization (by default there is a substitution of OWLAPI formats with Jena alternatives).
    But, axiom SameIndividual(x, x) is still illegal, and to create such construction need to switch to RDF API.

    Example:

        OWLOntologyManager m = OntManagers.createManager();

    OWLOntology ont = m.createOntology();
    String i = "http://i";

    OntModel g = ((Ontology) ont).asGraphModel();
    g.createIndividual(i).addSameIndividual(g.createIndividual(i));

    ont.saveOntology(new NTriplesDocumentFormat(), System.out);

    Output:

    <http://i> <http://www.w3.org/2002/07/owl#sameAs> <http://i> .
<http://i> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#NamedIndividual> .
_:B0ee0d3dfX2D1fe4X2D4489X2D9fc3X2De18bae6cfab4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Ontology> .