private void trAnnotations(Clause clause, Set<OWLAnnotation> anns) { Collection<Xref> xrefs = clause.getXrefs(); if (xrefs != null) { for (Xref x : xrefs) { if(x.getIdref() != null && x.getIdref().length()>0){ OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_XREF.getTag()); OWLAnnotation ann = fac.getOWLAnnotation(ap, trLiteral(x)); anns.add(ann); } } } Collection<QualifierValue> qvs = clause.getQualifierValues(); if (qvs != null) { for (QualifierValue qv : qvs) { String qTag = qv.getQualifier(); if (qTag.equals("gci_relation") || qTag.equals("gci_filler") || qTag.equals("cardinality") || qTag.equals("minCardinality") || qTag.equals("maxCardinality") || qTag.equals("all_some") || qTag.equals("all_only")) { continue; } OWLAnnotationProperty ap = trTagToAnnotationProp(qTag); OWLAnnotation ann = fac.getOWLAnnotation(ap, trLiteral(qv.getValue())); anns.add(ann); } } }
private OWLAnnotationProperty trTagToAnnotationProp(String tag) { IRI iri = trTagToIRI(tag); OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri); if (!apToDeclare.contains(ap)) { apToDeclare.add(ap); add(fac.getOWLDeclarationAxiom(ap)); Obo2OWLVocabulary vocab = Obo2OWLConstants.getVocabularyObj(tag); if(vocab != null){ add (fac.getOWLAnnotationAssertionAxiom(fac.getRDFSLabel(), iri, trLiteral( vocab.getLabel()) ) ); } } return ap; }
OWLAnnotation ann = fac.getOWLAnnotation(trAnnotationProp(IRI_PROP_isReversiblePropertyChain), trLiteral("true")); annotations.add(ann);
trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), annotations); trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), annotations); trSynonymType(synType), sub, trLiteral(clause.getValue()), annotations); trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), annotations); trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), annotations);
trTagToAnnotationProp("shorthand"), p.getIRI(), trLiteral(id), new HashSet<OWLAnnotation>());
add(fac.getOWLAnnotationAssertionAxiom(ap, childAnnotProp.getIRI(), trLiteral(clause.getValue2()))); add(fac.getOWLAnnotationAssertionAxiom(ap, childIRI, trLiteral( values[1] ))); addOntologyAnnotation(trTagToAnnotationProp(t), trLiteral(dateString), trAnnotations(clause)); addOntologyAnnotation(fac.getRDFSComment(), trLiteral(clause.getValue()), trAnnotations(clause)); addOntologyAnnotation(trTagToAnnotationProp(t), trLiteral(clause.getValue()), trAnnotations(clause));
trTagToAnnotationProp("shorthand"), p.getIRI(), trLiteral(id), new HashSet<OWLAnnotation>());