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

Example 51 with OWLOntology

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

the class TestOWLAPIInputSources method testOfflineImport.

/**
     * Uses a {@link ParentPathInputSource} to load an ontology importing a modified FOAF, both located in the
     * same resource directory.
     * 
     * @throws Exception
     */
@Test
public void testOfflineImport() throws Exception {
    URL url = getClass().getResource("/ontologies/maincharacters.owl");
    assertNotNull(url);
    File f = new File(url.toURI());
    assertNotNull(f);
    OntologyInputSource<OWLOntology> coreSource = new ParentPathInputSource(f);
    // // Check that all the imports closure is made of local files
    // Set<OWLOntology> closure = coreSource.getImports(true);
    // for (OWLOntology o : closure)
    // assertEquals("file", o.getOWLOntologyManager().getOntologyDocumentIRI(o).getScheme());
    assertEquals(coreSource.getRootOntology().getOntologyID().getOntologyIRI(), IRI.create(Constants.PEANUTS_MAIN_BASE));
    // Linus is stated to be a foaf:Person
    OWLNamedIndividual iLinus = df.getOWLNamedIndividual(IRI.create(Constants.PEANUTS_MAIN_BASE + "#Linus"));
    // Lucy is stated to be a foaf:Perzon
    OWLNamedIndividual iLucy = df.getOWLNamedIndividual(IRI.create(Constants.PEANUTS_MAIN_BASE + "#Lucy"));
    OWLClass cPerzon = df.getOWLClass(IRI.create("http://xmlns.com/foaf/0.1/Perzon"));
    Set<OWLIndividual> instances = cPerzon.getIndividuals(coreSource.getRootOntology());
    assertTrue(!instances.contains(iLinus) && instances.contains(iLucy));
}

Example 52 with OWLOntology

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

the class TestOWLAPIInputSources method testOfflineSingleton.

/**
     * Loads a modified FOAF by resolving a URI from a resource directory.
     * 
     * @throws Exception
     */
@Test
public void testOfflineSingleton() throws Exception {
    URL url = getClass().getResource("/ontologies/mockfoaf.rdf");
    assertNotNull(url);
    OntologyInputSource<OWLOntology> coreSource = new RootOntologySource(IRI.create(url));
    assertNotNull(df);
    /*
         * To check it fetched the correct ontology, we look for a declaration of the bogus class foaf:Perzon
         * (added in the local FOAF)
         */
    OWLClass cPerzon = df.getOWLClass(IRI.create("http://xmlns.com/foaf/0.1/Perzon"));
    assertTrue(coreSource.getRootOntology().getClassesInSignature().contains(cPerzon));
}

Example 53 with OWLOntology

use of org.semanticweb.owlapi.model.OWLOntology in project opentheso by miledrousset.

the class testApiSkosOfficial method testingOWL.

// TODO add test methods here.
// The methods must be annotated with annotation @Test. For example:
// 
// @Test
// public void hello() {}
/*
 * Copyright (C) 2007, University of Manchester
 *
 * Modifications to the initial code base are copyright of their
 * respective authors, or their employers as appropriate.  Authorship
 * of the modifications may be determined from the ChangeLog placed at
 * the end of this file.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.

 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.

 * You should have received a copy of the GNU Lesser General Public
 * License along with this library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
/**
 * Author: Simon Jupp<br>
 * Date: Mar 17, 2008<br>
 * The University of Manchester<br>
 * Bio-Health Informatics Group<br>
 */
// @Test
public void testingOWL() throws OWLOntologyCreationException, OWLOntologyStorageException {
    // Get hold of an ontology manager
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    // Load an ontology from the Web.  We load the ontology from a document IRI
    IRI docIRI = IRI.create("http://www.w3.org/2009/08/skos-reference/skos.rdf");
    OWLOntology skos = manager.loadOntologyFromOntologyDocument(docIRI);
    System.out.println("Loaded ontology: " + skos);
    System.out.println();
    // Save a local copy of the ontology.  (Specify a path appropriate to your setup)
    File file = new File("/Users/Miled/Downloads/downloadAndSaveOWLFile.owl");
    manager.saveOntology(skos, IRI.create(file.toURI()));
    // Ontologies are saved in the format from which they were loaded.
    // We can get information about the format of an ontology from its manager
    OWLOntologyFormat format = (OWLOntologyFormat) manager.getOntologyFormat(skos);
    System.out.println("    format: " + format);
    System.out.println();
    // Save the ontology in owl/xml format
    OWLXMLOntologyFormat owlxmlFormat = new OWLXMLOntologyFormat();
    // so that we have nicely abbreviated IRIs in the new ontology document
    if (format.isPrefixOWLOntologyFormat()) {
        owlxmlFormat.copyPrefixesFrom(format.asPrefixOWLOntologyFormat());
    }
    // manager.saveOntology(skos, (OWLOntologyFormat) (OWLDocumentFormat) owlxmlFormat, IRI.create(file.toURI()));
    // Dump an ontology to System.out by specifying a different OWLOntologyOutputTarget
    // Note that we can write an ontology to a stream in a similar way
    // using the StreamOutputTarget class
    OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
    // Try another format - The Manchester OWL Syntax
    ManchesterOWLSyntaxOntologyFormat manSyntaxFormat = new ManchesterOWLSyntaxOntologyFormat();
    if (format.isPrefixOWLOntologyFormat()) {
        manSyntaxFormat.copyPrefixesFrom(format.asPrefixOWLOntologyFormat());
    }
// manager.saveOntology(skos, (OWLOntologyFormat) (OWLDocumentFormat) manSyntaxFormat, documentTarget);
}

Example 54 with OWLOntology

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

the class DefaultGWASOWLPublisher method publishGWASData.

public OWLOntology publishGWASData() throws OWLConversionException {
    // create new ontology
    OWLOntology conversion = getConverter().createConversionOntology();
    // grab all studies from the DAO
    getLog().debug("Fetching studies that require conversion to OWL using StudyRepository...");
    Collection<Study> studies = getStudyService().deepFindPublishedStudies();
    //TODO : check with Tony probably better to do it at the Repository/Service level
    //Discard studies which are not associated with a disease trait and those which haven't been published yet
    //by the GWAS catalog.
    Iterator<Study> iterator = studies.iterator();
    while (iterator.hasNext()) {
        Study study = iterator.next();
        //Remove study which have no diseaseTrait.
        if (study.getDiseaseTrait() == null) {
            iterator.remove();
            getLog().error("Study '" + study.getId() + "' has no disease trait");
        } else if (study.getHousekeeping().getCatalogPublishDate() == null) {
            iterator.remove();
            getLog().error("Study '" + study.getId() + "' has not yet been published");
        } else //Remove studies that have been unpublished
        if (study.getHousekeeping().getCatalogUnpublishDate() != null) {
            iterator.remove();
            getLog().error("Study '" + study.getId() + "' has been unpublished");
        }
    //            }else {
    //
    //                //Remove study which have no associations where pvalue is not null.
    //                Collection<Association> associations = study.getAssociations();
    //                Iterator<Association> associationIterator = associations.iterator();
    //                int associationCount = 0;
    //                while (associationIterator.hasNext()) {
    //                    Association association = associationIterator.next();
    //
    //                    if (association.getPvalueExponent() != null && association.getPvalueMantissa() != null) {
    //                        associationCount++;
    //                    }
    //                }
    //                if (associationCount == 0) {
    //                    iterator.remove();
    //                }
    //            }
    }
    getLog().debug("Query complete, got " + studies.size() + " studies");
    // if studies limit is not set, convert all data, else filter to first n studies and associated data
    if (getStudiesLimit() == -1 && FilterProperties.getDateFilter() == null && FilterProperties.getPvalueFilter() == null) {
        System.out.println("Converting all available data");
        // grab all other data from the DAO
        getLog().debug("Fetching traits that require conversion to OWL using AssociationRepository...");
        Collection<Association> traitAssociations = getAssociationService().findReallyAll();
        //TODO check with Tony how to do that in a better way from service or repository (how to not get associations linked to study with no trait.
        //Discard all the associations which are linked to study which are not linked to a disease trait or haven't
        //been published yet in the GWAS catalog.
        Iterator<Association> associationIterator = traitAssociations.iterator();
        while (associationIterator.hasNext()) {
            Association association = associationIterator.next();
            if (association.getStudy().getDiseaseTrait() == null) {
                associationIterator.remove();
            } else if (association.getStudy().getHousekeeping().getCatalogPublishDate() == null) {
                associationIterator.remove();
            } else if (association.getStudy().getHousekeeping().getCatalogUnpublishDate() != null) {
                associationIterator.remove();
            }
        }
        getLog().debug("Fetching SNPs that require conversion to OWL using SingleNucleotidePolymorphismRepository...");
        Collection<SingleNucleotidePolymorphism> snps = getSingleNucleotidePolymorphismService().findAll();
        getLog().debug("All data fetched");
        // convert this data, starting with SNPs (no dependencies) and working up to studies
        getLog().debug("Starting conversion to OWL...");
        getLog().debug("Converting SNPs...");
        getConverter().addSNPsToOntology(snps, conversion);
        getLog().debug("Converting Trait Associations...");
        getConverter().addAssociationsToOntology(traitAssociations, conversion);
        getLog().debug("Converting Studies...");
        getConverter().addStudiesToOntology(studies, conversion);
        getLog().debug("All conversion done!");
        return conversion;
    } else {
        System.out.println("Data conforming to the filter only");
        return filterAndPublishGWASData(conversion, studies);
    }
}

Example 55 with OWLOntology

use of org.semanticweb.owlapi.model.OWLOntology 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;
}