List of loadOntology() Examples

Examples of loadOntology()

bnGUI.OBOES.loadOntology()
eneontology.org/GO.format.shtml#oboflat">http://www.geneontology.org/GO.format.shtml#oboflat for a description of the OBO file format. The OBO for GO can be found online at http://www.geneontology.org. Ontologies loaded by loadOntology can be retrieved through the getOntology function of OBOES.
When loading an ontology, you must specify the path to the OBO file representing the ontology, as well as a user-specified name or handle to the ontology. Ontology names are arbitrary, but it is suggested that they bear some semblance to the actual name of the ontology. You cannot specify the same ontology name to be loaded twice for the same OBOES object. An ontology cannot be unloaded from an existing OBOES object after it is loaded; instead, simply create a new OBOES object. The OBO file path can be a local file, or it can be an online file. If the file is online, the full URL must be used, including the "http://" or "ftp://" prefix. @param OBOFile the path to the OBO file to read in @param ontology_name the user-specified name/handle to give to this ontology @return true if the specified OBO file was read in without problems. falseif a problem was encountered; an error message is also displayed. @see Ontology
edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology.loadOntology()
load index finder tables from an IOntology object @param ontology @throws IOException @throws TerminologyException
edu.pitt.terminology.client.IndexFinderTerminology.loadOntology()
load index finder tables from an IOntology object @param ontology @throws IOException @throws TerminologyException
enzyme.ontology.OntologyDataSource.loadOntology()
org.mindswap.pellet.owlapi.Reasoner.loadOntology()
org.semanticweb.owl.model.OWLOntologyManager.loadOntology()
Loads the ontology specified by the ontologyURI parameter. Note that this is NOT the physical URI that points to a concrete representation (e.g. an RDF/XML OWL file) of an ontology. The mapping to a physical URI will be determined by using one of the loaded OWLOntologyURIMappers. @param ontologyURI The ontology URI (sometimes called logical URI of the ontology to be loaded) @return The OWLOntology representation of the ontology that was loaded. If an ontology with thespecified URI is already loaded then that ontology will be returned. @throws OWLOntologyCreationException If there was a problem in creating and loading the ontology.
org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()
Loads an ontology that is assumed to have the specified {@code ontologyIRI} as its IRI or version IRI.
The ontology IRI will be mapped to an ontology document IRI. The mapping will be determined using one of the loaded {@link OWLOntologyIRIMapper}objects. By default, if no custom {@code OWLOntologyIRIMapper}s have been registered using the {@link #getIRIMappers()} PriorityCollection{@link PriorityCollection#add(Serializable)} method, or no mapping canbe found, the ontology document IRI is taken to be the specified ontology IRI. @param ontologyIRI The IRI that identifies the ontology. It is expected that the ontology will also have this IRI (although the OWL API will tolerated situations where this is not the case). @return The {@code OWLOntology} representation of the ontology that wasloaded. @throws OWLOntologyCreationException If there was a problem in creating and loading the ontology. @throws org.semanticweb.owlapi.io.UnparsableOntologyException if the ontology was being parsed from a document and the document contained syntax errors. @throws UnloadableImportException if the ontology imports ontologies and one of the imports could not be loaded for what ever reason. If the {@link MissingImportHandlingStrategy} is set to{@link MissingImportHandlingStrategy#SILENT} then this exceptionwill not be thrown. The {@code UnloadableImportException}contains information about the import declaration that triggered the import and the cause of this exception is an {@code OWLOntologyCreationException} which contains informationabout why the import could not be loaded. @throws org.semanticweb.owlapi.io.OWLOntologyCreationIOException if there was an {@code IOException} when trying to load theontology. @throws OWLOntologyAlreadyExistsException if the manager already contains an ontology with the specified {@code ontologyIRI} (where the ontology doesn't have a versionIRI). @throws OWLOntologyDocumentAlreadyExistsException if the specified {@code ontologyIRI} is mapped to a ontologydocument IRI for which there already exists a mapping in this manager.

Examples of org.semanticweb.owl.model.OWLOntologyManager.loadOntology()

    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    
    OWLOntology tbox = null, abox = null;
    try {
      
      tbox = manager.loadOntology(tboxURI);
      abox = manager.loadOntology(aboxURI);
      
      // Compute the number of direct individuals for each class
      for (OWLClass owlClass : v)
      {

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Examples of org.semanticweb.owl.model.OWLOntologyManager.loadOntology()

    
    OWLOntology tbox = null, abox = null;
    try {
      
      tbox = manager.loadOntology(tboxURI);
      abox = manager.loadOntology(aboxURI);
      
      // Compute the number of direct individuals for each class
      for (OWLClass owlClass : v)
      {
        fillScores(owlClass, 1.0 * owlClass.getIndividuals(abox).size(), tbox, MAX_STEP);

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Examples of org.semanticweb.owl.model.OWLOntologyManager.loadOntology()

    // Compute the ordered list of classes
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    
    OWLOntology tbox = null;
    try {
      tbox = manager.loadOntology(tboxURI);
      
      // Compute the number of direct subclasses of each class
      for (OWLClass owlClass : this.classes){
        Set<OWLDescription> subClasses = owlClass.getSubClasses(tbox);
        this.sortedList.add(new OWLSubclass(owlClass,subClasses.size()));

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Examples of org.semanticweb.owl.model.OWLOntologyManager.loadOntology()

    // Compute the ordered list of classes
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology tbox = null;
    
    try {
      tbox = manager.loadOntology(tboxURI);
      
      // Compute the number of direct subclasses of each class
      for (OWLClass owlClass : this.classes){
        Set<OWLDescription> subClasses = owlClass.getSubClasses(tbox);
        this.sortedList.add(new OWLSubclass(owlClass,subClasses.size()));

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Examples of org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()

        // Create a manager to work with
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        // Load the MGED ontology. There is a copy of the MGED ontology located
        // at the address pointed to by its ontology IRI (this is good practice
        // and is recommended in the OWL 2 spec).
        OWLOntology ontology = manager.loadOntology(mgedOntologyIri);
        // Print out the ontology IRI and its imported ontology IRIs
        printOntologyAndImports(manager, ontology);
        // We'll load the MGED ontology again, but this time, we'll get the
        // Protege ontology (that it imports) from the TONES repository. To tell
        // the ontology manager to do this we need to add an IRI mapper. We need

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Examples of org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()

        manager.getIRIMappers().add(new SimpleIRIMapper(iri, IRI.create(file)));
        // Load the ontology as if we were loading it from the web (from its
        // ontology IRI)
        IRI pizzaOntologyIRI = IRI
                .create("http://owl.cs.manchester.ac.uk/co-ode-files/ontologies/pizza.owl");
        OWLOntology redirectedPizza = manager.loadOntology(pizzaOntologyIRI);
        IRI pizza = manager.getOntologyDocumentIRI(redirectedPizza);
        // Note that when imports are loaded an ontology manager will be
        // searched for mappings
    }

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Examples of org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()


    @Test
    public void testRemoteIsParseable() throws OWLOntologyCreationException {
        OWLOntologyManager manager = getManager();
        IRI iri = IRI(str);
        OWLOntology ontology = manager.loadOntology(iri);
        assertEquals(1, ontology.getAxioms().size());
        assertEquals(ontology.getOntologyID().getOntologyIRI().get(), iri);
        assertNotNull(manager.getOntology(iri));
    }

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Examples of org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()

    public void testEquivalentLoading() throws OWLOntologyCreationException {
        OWLOntologyManager managerStart = getManager();
        OWLOntology manualImport = managerStart
                .loadOntologyFromOntologyDocument(new File(RESOURCES, superpath));
        OWLOntologyManager managerTest = getManager();
        OWLOntology iriImport = managerTest.loadOntology(IRI(str));
        assertEquals(manualImport.getAxioms(), iriImport.getAxioms());
        assertEquals(manualImport.getOntologyID(), iriImport.getOntologyID());
    }


    @Test

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Examples of org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()

        }
        public void run(Reasoner hermit,Prefixes prefixes,StatusOutput status,PrintWriter output) {
            status.log(2,"Checking whether the loaded ontology entails the conclusion ontology");
            OWLOntologyManager m=OWLManager.createOWLOntologyManager();
            try {
                OWLOntology conclusions = m.loadOntology(conclusionIRI);
                EntailmentChecker checker=new EntailmentChecker(hermit, m.getOWLDataFactory());
                boolean isEntailed=checker.entails(conclusions.getLogicalAxioms());
                output.println(isEntailed);
            } catch (OWLOntologyCreationException e) {
                e.printStackTrace();

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Examples of org.semanticweb.owlapi.model.OWLOntologyManager.loadOntology()

                status.log(2,"Processing "+ont.toString());
                status.log(2,String.valueOf(actions.size())+" actions");
                try {
                    long startTime=System.currentTimeMillis();
                    OWLOntologyManager ontologyManager=OWLManager.createOWLOntologyManager();
                    OWLOntology ontology=ontologyManager.loadOntology(ont);
                    long parseTime=System.currentTimeMillis()-startTime;
                    status.log(2,"Ontology parsed in "+String.valueOf(parseTime)+" msec.");
                    startTime=System.currentTimeMillis();
                    Reasoner hermit=new Reasoner(config,ontology);
                    long loadTime=System.currentTimeMillis()-startTime;

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