Examples with OWLClass org.semanticweb.owlapi.model.OWLClass used on opensource projects

Example 16 with OWLClass

use of org.semanticweb.owlapi.model.OWLClass in project stanbol by apache.

the class ConversionTester method testAxiomOwlToJenaResource.

public void testAxiomOwlToJenaResource() {
    JenaToOwlConvert j2o = new JenaToOwlConvert();
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLOntology ont = null;
    try {
        ont = mgr.createOntology();
    } catch (OWLOntologyCreationException e) {
        e.printStackTrace();
        fail("Can not create ontology");
    }
    OWLDataFactory factory = mgr.getOWLDataFactory();
    StmtIterator resource = null;
    OWLClass cls = factory.getOWLClass(IRI.create(CLAZZ));
    OWLDataProperty dp = factory.getOWLDataProperty(IRI.create(DP));
    OWLObjectProperty op = factory.getOWLObjectProperty(IRI.create(OP));
    OWLAnnotationProperty oa = factory.getOWLAnnotationProperty(IRI.create(label));
    OWLAnnotation oav = factory.getOWLAnnotation(oa, factory.getOWLStringLiteral(clazzlabel, "en"));
    OWLDatatype dt = factory.getOWLDatatype(IRI.create(DATATYPE));
    OWLNamedIndividual sub = factory.getOWLNamedIndividual(IRI.create(SUBJECT));
    OWLNamedIndividual obj = factory.getOWLNamedIndividual(IRI.create(OBJECT));
    OWLLiteral literal1 = factory.getOWLTypedLiteral(VALUE, dt);
    // Classe
    OWLDeclarationAxiom daxiomcls = factory.getOWLDeclarationAxiom(cls);
    // obj prop
    OWLDeclarationAxiom daxiomop = factory.getOWLDeclarationAxiom(op);
    // data prop
    OWLDeclarationAxiom daxiomdp = factory.getOWLDeclarationAxiom(dp);
    // subject
    OWLDeclarationAxiom daxiomsub = factory.getOWLDeclarationAxiom(sub);
    // object
    OWLDeclarationAxiom daxiomobj = factory.getOWLDeclarationAxiom(obj);
    // Istanza
    OWLClassAssertionAxiom axiomsub = factory.getOWLClassAssertionAxiom(cls, sub);
    // Istanza
    OWLClassAssertionAxiom axiomobj = factory.getOWLClassAssertionAxiom(cls, obj);
    // Obj
    OWLObjectPropertyAssertionAxiom axiomop = factory.getOWLObjectPropertyAssertionAxiom(op, sub, obj);
    // prop
    // tra
    // individui
    OWLDataPropertyAssertionAxiom axiomvalue = factory.getOWLDataPropertyAssertionAxiom(dp, obj, // Dataprop all'istanza;
    literal1);
    // Annotazione
    OWLAnnotationAssertionAxiom axioman = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), oav);
    mgr.addAxiom(ont, daxiomcls);
    mgr.addAxiom(ont, daxiomop);
    mgr.addAxiom(ont, daxiomdp);
    mgr.addAxiom(ont, daxiomsub);
    mgr.addAxiom(ont, daxiomobj);
    mgr.addAxiom(ont, axiomsub);
    mgr.addAxiom(ont, axiomobj);
    mgr.addAxiom(ont, axiomop);
    mgr.addAxiom(ont, axiomvalue);
    mgr.addAxiom(ont, axioman);
    Set<OWLAxiom> setaxiom = ont.getAxioms();
    try {
        resource = j2o.AxiomOwlToJenaResource(setaxiom, RDFXML);
        if (resource == null) {
            fail("Some errors occur");
        } else {
            String statment = "[http://www.w3.org/2000/01/rdf-schema#label, http://www.w3.org/2000/01/rdf-schema#range, http://www.w3.org/2000/01/rdf-schema#Literal] " + "[http://example.org/dummy#hasAge, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#DatatypeProperty] " + "[http://example.org/dummy#Linus, http://example.org/dummy#hasAge, \"8\"^^http://www.w3.org/2001/XMLSchema#int] " + "[http://example.org/dummy#Linus, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://example.org/dummy#Peanut] " + "[http://example.org/dummy#hasSibling, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#ObjectProperty] " + "[http://example.org/dummy#Lucy, http://example.org/dummy#hasSibling, http://example.org/dummy#Linus] " + "[http://example.org/dummy#Lucy, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://example.org/dummy#Peanut] " + "[http://www.w3.org/2000/01/rdf-schema#label, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#AnnotationProperty] " + "[http://example.org/dummy#Peanut, http://www.w3.org/2000/01/rdf-schema#label, \"Peanut\"@en] " + "[http://example.org/dummy#Peanut, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/2002/07/owl#Class]";
            int size = setaxiom.size();
            int count = 0;
            while (resource.hasNext()) {
                Statement stm = resource.nextStatement();
                Resource jsubj = stm.getSubject();
                if (jsubj.getURI().equals(OP.toString()) || jsubj.getURI().equals(DP.toString()) || jsubj.getURI().equals(CLAZZ.toString()) || jsubj.getURI().equals(OBJECT.toString()) || jsubj.getURI().equals(SUBJECT.toString()) || jsubj.getURI().equals(label.toString()))
                    if (statment.contains(stm.toString()))
                        count++;
            }
            assertEquals(size, count);
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail("Exception caugth");
    } finally {
        assertNotNull(resource);
    }
}

Example 17 with OWLClass

use of org.semanticweb.owlapi.model.OWLClass in project stanbol by apache.

the class ConversionTester method testClassOwlToJena.

public void testClassOwlToJena() {
    JenaToOwlConvert j2o = new JenaToOwlConvert();
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = mgr.getOWLDataFactory();
    OWLClass c = factory.getOWLClass(IRI.create(CLAZZ));
    OntClass jc = null;
    try {
        jc = j2o.ClassOwlToJena(c, RDFXML);
        if (jc == null) {
            fail("Some problem accours");
        } else {
            assertEquals(jc.getURI(), c.getIRI().toString());
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail("Exception caught");
    } finally {
        assertNotNull(jc);
    }
}

Example 18 with OWLClass

use of org.semanticweb.owlapi.model.OWLClass in project goci by EBISPOT.

the class DefaultGWASOWLConverter method convertStudy.

protected void convertStudy(Study study, OWLOntology ontology) {
    // get the study class
    OWLClass studyCls = getDataFactory().getOWLClass(IRI.create(OntologyConstants.STUDY_CLASS_IRI));
    // create a new study instance
    OWLNamedIndividual studyIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, study));
    // assert class membership
    OWLClassAssertionAxiom classAssertion = getDataFactory().getOWLClassAssertionAxiom(studyCls, studyIndiv);
    getManager().addAxiom(ontology, classAssertion);
    // add datatype properties...
    // get datatype relations
    OWLDataProperty has_author = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_AUTHOR_PROPERTY_IRI));
    OWLDataProperty has_publication_date = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_PUBLICATION_DATE_PROPERTY_IRI));
    OWLDataProperty has_pubmed_id = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_PUBMED_ID_PROPERTY_IRI));
    // get annotation relations
    OWLAnnotationProperty rdfsLabel = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    // assert author relation
    OWLLiteral author = getDataFactory().getOWLLiteral(study.getAuthor());
    OWLDataPropertyAssertionAxiom author_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_author, studyIndiv, author);
    AddAxiom add_author = new AddAxiom(ontology, author_relation);
    getManager().applyChange(add_author);
    // assert publication_date relation
    if (study.getPublicationDate() != null) {
        String rfcTimezone = new SimpleDateFormat("Z").format(study.getPublicationDate());
        String xsdTimezone = rfcTimezone.substring(0, 3).concat(":").concat(rfcTimezone.substring(3, rfcTimezone.length()));
        String xmlDatetimeStr = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").format(study.getPublicationDate()) + xsdTimezone;
        OWLLiteral publication_date = getDataFactory().getOWLLiteral(xmlDatetimeStr, OWL2Datatype.XSD_DATE_TIME);
        OWLDataPropertyAssertionAxiom publication_date_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_publication_date, studyIndiv, publication_date);
        AddAxiom add_publication_date = new AddAxiom(ontology, publication_date_relation);
        getManager().applyChange(add_publication_date);
    }
    // assert pubmed_id relation
    OWLLiteral pubmed_id = getDataFactory().getOWLLiteral(study.getPubmedId());
    OWLDataPropertyAssertionAxiom pubmed_id_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_pubmed_id, studyIndiv, pubmed_id);
    AddAxiom add_pubmed_id = new AddAxiom(ontology, pubmed_id_relation);
    getManager().applyChange(add_pubmed_id);
    // assert label
    OWLLiteral study_label = getDataFactory().getOWLLiteral(pubmed_id.toString());
    OWLAnnotationAssertionAxiom label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, studyIndiv.getIRI(), study_label);
    AddAxiom add_label = new AddAxiom(ontology, label_annotation);
    getManager().applyChange(add_label);
    // add object properties...
    // get the has_part relation
    OWLObjectProperty has_part = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_PART_PROPERTY_IRI));
    OWLObjectProperty part_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.PART_OF_PROPERTY_IRI));
    // for this study, get all trait associations 
    Collection<Association> associations = study.getAssociations();
    // and create an study has_part association assertion for each one
    for (Association association : associations) {
        // get the trait association instance for this association
        IRI traitIRI = getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, association);
        OWLNamedIndividual taIndiv = getDataFactory().getOWLNamedIndividual(traitIRI);
        // assert relation
        OWLObjectPropertyAssertionAxiom has_part_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_part, studyIndiv, taIndiv);
        AddAxiom addAxiomChange = new AddAxiom(ontology, has_part_relation);
        getManager().applyChange(addAxiomChange);
        OWLObjectPropertyAssertionAxiom is_part_of_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(part_of, taIndiv, studyIndiv);
        AddAxiom addAxiomChangeRev = new AddAxiom(ontology, is_part_of_relation);
        getManager().applyChange(addAxiomChangeRev);
    }
}

Example 19 with OWLClass

use of org.semanticweb.owlapi.model.OWLClass in project goci by EBISPOT.

the class ParentMappingService method findParent.

public String findParent(String term) {
    String parent = null;
    OWLClass cls = ontologyLoader.getFactory().getOWLClass(IRI.create(term));
    Set<OWLClass> parents = ontologyLoader.getOWLReasoner().getSuperClasses(cls, false).getFlattened();
    Set<String> available = ParentList.PARENT_URI.keySet();
    OWLClass leaf = null;
    int largest = 0;
    if (parents.size() == 2) {
        System.out.println("Trait " + term + " is not mapped");
        getLog().debug("Trait " + term + " is not mapped");
    } else {
        for (OWLClass t : parents) {
            String iri = t.getIRI().toString();
            int allp = ontologyLoader.getOWLReasoner().getSuperClasses(t, false).getFlattened().size();
            if (allp > largest && available.contains(iri)) {
                largest = allp;
                leaf = t;
            }
        }
        if (leaf != null) {
            parent = leaf.getIRI().toString();
        } else {
            System.out.println("Could not identify a suitable  parent category for trait " + term);
            getLog().debug("Could not identify a suitable  parent category for trait " + term);
        }
    }
    return parent;
}

Example 20 with OWLClass

use of org.semanticweb.owlapi.model.OWLClass in project goci by EBISPOT.

the class IRITreeBuilder method buildIRITree.

//    OntologyLoader ontologyLoader;
//
//    @Autowired
//    public IRITreeBuilder(OntologyLoader ontologyLoader){
//        this.ontologyLoader = ontologyLoader;
//    }
public IRITree buildIRITree(URL efoLocation) throws URISyntaxException, OWLOntologyCreationException {
    // load efo
    getLog().info("Loading efo...");
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology efo = manager.loadOntology(IRI.create(efoLocation));
    owlNothingIRI = manager.getOWLDataFactory().getOWLNothing().getIRI().toString();
    // create a reasoner over efo
    getLog().info("Reasoning over efo...");
    OWLReasonerFactory factory = new Reasoner.ReasonerFactory();
    ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor();
    OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor);
    OWLReasoner reasoner = factory.createReasoner(efo, config);
    getLog().info("Precomputing inferences...");
    reasoner.precomputeInferences();
    getLog().info("Checking ontology consistency...");
    reasoner.isConsistent();
    // get 'top' class
    OWLClass topClass = reasoner.getTopClassNode().getRepresentativeElement();
    getLog().info("Reasoner 'top class' element is " + topClass.getIRI());
    IRITree tree = new IRITree();
    // do one level deep manually - should only be experimental factor
    IRINode rootNode = null;
    OWLClass efClass = null;
    NodeSet<OWLClass> subclasses = reasoner.getSubClasses(topClass, true);
    for (Node<OWLClass> node : subclasses) {
        OWLClass cls = node.getRepresentativeElement();
        getLog().debug("Next child of " + topClass + " is " + cls);
        if (cls.getIRI().toString().equals(OntologyConstants.EXPERIMENTAL_FACTOR_CLASS_IRI)) {
            efClass = cls;
            rootNode = new IRINode(cls.getIRI(), getClassLabel(efo, cls));
        }
    }
    if (rootNode != null) {
        getLog().info("Building tree... walking ontology from " + rootNode.getLabel() + " down...");
        tree.setRootNode(rootNode);
        recurse(reasoner, efo, efClass, rootNode);
        getLog().info("...Tree build complete!");
    } else {
        throw new RuntimeException("Could not find Experimental Factor as a child of OWL:Thing");
    }
    return tree;
}