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);
}
}
}
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);
}
}
