コード例 #1
0
 private void translateMatrixCell(
     Taxon taxon, Character character, State state, OWLNamedIndividual matrixCell) {
   this.addClass(matrixCell, this.factory.getOWLClass(IRI.create(CDAO.MATRIX_CELL)));
   this.addPropertyAssertion(
       IRI.create(CDAO.BELONGS_TO_CHARACTER), matrixCell, this.characterToOWLMap.get(character));
   this.addPropertyAssertion(
       IRI.create(CDAO.BELONGS_TO_TU), matrixCell, this.taxonOTUToOWLMap.get(taxon));
   this.addPropertyAssertion(
       IRI.create(CDAO.HAS_STATE), matrixCell, this.stateToOWLMap.get(state));
   if (taxon.getValidName() != null) {
     final IRI taxonIRI = this.convertOBOIRI(taxon.getValidName().getID());
     final OWLClass taxonClass = this.factory.getOWLClass(taxonIRI);
     for (Phenotype phenotype : state.getPhenotypes()) {
       final OWLClass eq = this.phenotypeToOWLMap.get(phenotype);
       final OWLObjectProperty exhibits =
           this.factory.getOWLObjectProperty(IRI.create(PHENOSCAPE.EXHIBITS));
       final OWLClassExpression exhibitsSomeEQ =
           this.factory.getOWLObjectSomeValuesFrom(exhibits, eq);
       final OWLAnnotationProperty positedBy =
           this.factory.getOWLAnnotationProperty(IRI.create(PHENOSCAPE.POSITED_BY));
       final OWLAnnotation positedByAnnotation =
           this.factory.getOWLAnnotation(positedBy, matrixCell.getIRI());
       final Set<OWLAnnotation> annotations = Collections.singleton(positedByAnnotation);
       final OWLSubClassOfAxiom annotatedSubClassOfAxiom =
           this.factory.getOWLSubClassOfAxiom(taxonClass, exhibitsSomeEQ, annotations);
       this.ontologyManager.addAxiom(this.ontology, annotatedSubClassOfAxiom);
     }
   }
 }
コード例 #2
0
 private void translateTaxon(Taxon taxon, OWLNamedIndividual otu) {
   this.taxonOTUToOWLMap.put(taxon, otu);
   this.addClass(otu, this.factory.getOWLClass(IRI.create(CDAO.OTU)));
   if (StringUtils.isNotBlank(taxon.getPublicationName())) {
     final OWLLiteral label = this.factory.getOWLLiteral(taxon.getPublicationName());
     this.addAnnotation(OWLRDFVocabulary.RDFS_LABEL.getIRI(), otu.getIRI(), label);
   }
   if (taxon.getValidName() != null) {
     final IRI taxonIRI = this.convertOBOIRI(taxon.getValidName().getID());
     this.addClass(
         this.factory.getOWLNamedIndividual(taxonIRI),
         this.factory.getOWLClass(IRI.create(PHENOSCAPE.TAXON)));
     this.addPropertyAssertion(
         IRI.create(CDAO.HAS_EXTERNAL_REFERENCE),
         otu,
         this.factory.getOWLNamedIndividual(taxonIRI));
   }
   if (StringUtils.isNotBlank(taxon.getComment())) {
     final OWLLiteral comment = factory.getOWLLiteral(taxon.getComment());
     this.addAnnotation(OWLRDFVocabulary.RDFS_COMMENT.getIRI(), otu.getIRI(), comment);
   }
   for (Specimen specimen : taxon.getSpecimens()) {
     final OWLAnonymousIndividual owlSpecimen = this.factory.getOWLAnonymousIndividual();
     this.addPropertyAssertion(IRI.create(DWC.HAS_SPECIMEN), otu, owlSpecimen);
     this.translateSpecimen(specimen, owlSpecimen);
   }
 }