private void translateState(State state, OWLNamedIndividual owlState) {
this.stateToOWLMap.put(state, owlState);
this.addClass(owlState, this.factory.getOWLClass(IRI.create(CDAO.STANDARD_STATE)));
if (StringUtils.isNotBlank(state.getLabel())) {
final OWLLiteral label = this.factory.getOWLLiteral(state.getLabel());
this.addAnnotation(OWLRDFVocabulary.RDFS_LABEL.getIRI(), owlState.getIRI(), label);
}
if (StringUtils.isNotBlank(state.getComment())) {
final OWLLiteral comment = factory.getOWLLiteral(state.getComment());
this.addAnnotation(OWLRDFVocabulary.RDFS_COMMENT.getIRI(), owlState.getIRI(), comment);
}
int phenotypeIndex = 0;
final OWLObjectProperty denotes = this.factory.getOWLObjectProperty(IRI.create(IAO.DENOTES));
for (Phenotype phenotype : state.getPhenotypes()) {
phenotypeIndex++;
final IRI phenotypeIRI =
IRI.create(owlState.getIRI().toURI().toString() + "/phenotype/" + phenotypeIndex);
final OWLClass owlPhenotype = this.factory.getOWLClass(phenotypeIRI);
final OWLObjectAllValuesFrom denotesOnlyPhenotype =
this.factory.getOWLObjectAllValuesFrom(denotes, owlPhenotype);
this.ontologyManager.addAxiom(
ontology, this.factory.getOWLClassAssertionAxiom(denotesOnlyPhenotype, owlState));
this.translatePhenotype(phenotype, owlPhenotype);
}
}
