private OWLAnnotationProperty trSynonymType(String type) { if (type.equals(OboFormatTag.TAG_RELATED.getTag()) || type.equals(OboFormatTag.TAG_EXACT.getTag()) || type.equals(OboFormatTag.TAG_NARROW.getTag()) || type.equals(OboFormatTag.TAG_BROAD.getTag())) { return trTagToAnnotationProp(type); } return trAnnotationProp(type); }
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); } } }
trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), trTagToAnnotationProp(tag), sub, trAnnotationProp(v.toString()).getIRI(), if(values.length>2){ OWLAnnotation ann= fac.getOWLAnnotation(trTagToAnnotationProp(OboFormatTag.TAG_HAS_SYNONYM_TYPE.getTag()), trAnnotationProp(values[2].toString()).getIRI()); annotations.add(ann); trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()), trTagToAnnotationProp(tag), sub, trLiteral(clause.getValue()),
OWLAnnotationProperty parentAnnotProp = trTagToAnnotationProp(t); OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_COMMENT.getTag()); add(fac.getOWLAnnotationAssertionAxiom(ap, childAnnotProp.getIRI(), trLiteral(clause.getValue2()))); OWLAnnotationProperty parentAnnotProp = trTagToAnnotationProp(t); add(fac.getOWLSubAnnotationPropertyOfAxiom(childAnnotProp, parentAnnotProp, annotations)); OWLAnnotationProperty ap = trTagToAnnotationProp(OboFormatTag.TAG_NAME.getTag()); add(fac.getOWLAnnotationAssertionAxiom(ap, childIRI, trLiteral( values[1] ))); ap = trTagToAnnotationProp(OboFormatTag.TAG_SCOPE.getTag()); add (fac.getOWLAnnotationAssertionAxiom(ap, childIRI, trTagToAnnotationProp( values[2].toString() ).getIRI() )); addOntologyAnnotation(trTagToAnnotationProp(t), trLiteral(dateString), trAnnotations(clause)); addOntologyAnnotation(trTagToAnnotationProp(t), trLiteral(clause.getValue()), trAnnotations(clause));
if (id.equals(xid) == false) { OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom( trTagToAnnotationProp("shorthand"), p.getIRI(), trLiteral(id),
if (xid.equals(id) == false) { OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom( trTagToAnnotationProp("shorthand"), p.getIRI(), trLiteral(id),