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 bnGUI.OBOES.loadOntology()

        myOB.setCorrectionMethod("benjamini_hochberg");
        myOB.setMaximumPvalue(.05);
        myOB.setMinimumCount(2);


        //This loads the data in
        myOB.loadOntology(ontology.getAbsolutePath(), "gene ontology");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "gene ontology");
        } catch (Exception ex) {

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Examples of edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology.loadOntology()

    IOntology ont = OOntology.loadOntology(url);
    ConceptRegistry.REGISTRY.put(url,SlideTutorConcept.class.getName());
    
    // create in-memory terminology from this ontology
    NobleCoderTerminology term = new NobleCoderTerminology();
    term.loadOntology(ont,null,true,true);
    term.setScoreConcepts(false);
    term.setSelectBestCandidate(false);
    term.setCachingEnabled(false);
    
    NobleCoderTerminology aterm = new NobleCoderTerminology();

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Examples of edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology.loadOntology()

    term.setScoreConcepts(false);
    term.setSelectBestCandidate(false);
    term.setCachingEnabled(false);
    
    NobleCoderTerminology aterm = new NobleCoderTerminology();
    aterm.loadOntology(OOntology.loadOntology(""+ANATOMY_ONTOLOGY_URI),null,true,true);
    aterm.setCachingEnabled(false);
    
    // add a terminology to it
    CompositTerminology terminology = new CompositTerminology();
    terminology.addTerminology(term);

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Examples of edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology.loadOntology()

      name = (name == null)?f.getName():name;
    }else if(owl != null){
      log("Loading OWL terminology from "+owl+"...");
      IOntology ont = OOntology.loadOntology(owl);
      if(ont != null){
        terminology.loadOntology(ont,name,false,abbreviateURI);
      }
      name = (name == null)?ont.getName():name;
    }else if(obo != null){
      log("Loading OBO terminology from "+obo+"...");
      if(name == null){

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Examples of edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology.loadOntology()

      log("Loading BioPortal terminology from "+bioportal+"...");
      BioPortalRepository r = new BioPortalRepository();
      IOntology ont = r.getOntology(URI.create(bioportal));
      if(ont != null){
        ont.addPropertyChangeListener(this);
        terminology.loadOntology(ont,name);
      }
      name = (name == null)?ont.getName():name;
    }else if(txt != null){
      log("Loading Text terminology from "+txt+"...");
      File f = new File(txt);

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Examples of edu.pitt.terminology.client.IndexFinderTerminology.loadOntology()

      name = (name == null)?f.getName():name;
    }else if(owl != null){
      log("Loading OWL terminology from "+owl+"...");
      IOntology ont = POntology.loadOntology(owl);
      if(ont != null){
        terminology.loadOntology(ont,name);
      }
      name = (name == null)?ont.getName():name;
    }else if(obo != null){
      log("Loading OBO terminology from "+obo+"...");
      if(name == null){

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Examples of edu.pitt.terminology.client.IndexFinderTerminology.loadOntology()

      log("Loading BioPortal terminology from "+bioportal+"...");
      BioPortalRepository r = new BioPortalRepository();
      IOntology ont = r.getOntology(URI.create(bioportal));
      if(ont != null){
        ont.addPropertyChangeListener(this);
        terminology.loadOntology(ont,name);
      }
      name = (name == null)?ont.getName():name;
    }else if(txt != null){
      log("Loading Text terminology from "+txt+"...");
      File f = new File(txt);

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Examples of edu.pitt.terminology.client.IndexFinderTerminology.loadOntology()

    IOntology ont = POntology.loadOntology(url);
    ConceptRegistry.REGISTRY.put(url,SlideTutorConcept.class.getName());
    
    // create in-memory terminology from this ontology
    IndexFinderTerminology term = new IndexFinderTerminology();
    term.loadOntology(ont,null,true,true);
    term.setScoreConcepts(false);
    term.setSelectBestCandidate(false);
    term.setCachingEnabled(false);
    
    IndexFinderTerminology aterm = new IndexFinderTerminology();

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Examples of edu.pitt.terminology.client.IndexFinderTerminology.loadOntology()

    term.setScoreConcepts(false);
    term.setSelectBestCandidate(false);
    term.setCachingEnabled(false);
    
    IndexFinderTerminology aterm = new IndexFinderTerminology();
    aterm.loadOntology(POntology.loadOntology(ANATOMY_ONTOLOGY_URI),null,true,true);
    aterm.setCachingEnabled(false);
    
    // add a terminology to it
    CompositTerminology terminology = new CompositTerminology();
    terminology.addTerminology(term);

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Examples of enzyme.ontology.OntologyDataSource.loadOntology()

    String weights = context.getRealPath("/bookshop/ontology/Weights.properties");
    
    //������������Դ����
    OntologyDataSource ods = new OntologyDataSource();
    //���ر����
    ods.loadOntology(ontology);
    //����ǰ׺����
    ods.loadPrefixConfiguration(prefix);
    
    //����Ȩֵ
    ods.setWeightsPath(weights);

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