Fix synonym type extraction in RDF/XML parser

althonos · Feb 21, 2024 · 51ef9b3 · 51ef9b3
1 parent 7566b5c
commit 51ef9b3
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Showing 2 changed files with 70 additions and 2 deletions.
diff --git a/pronto/parsers/rdfxml.py b/pronto/parsers/rdfxml.py
@@ -802,14 +802,27 @@ def _process_axiom(self, elem: etree.Element, curies: Dict[str, str]):
  )
  return
 
- type_ = elem.find(_NS["oboInOwl"]["hasSynonymType"])
+ # extract synonym type name or IRI
+ elem_type = elem.find(_NS["oboInOwl"]["hasSynonymType"])
+ if elem_type is None:
+ type_ = None
+ elif _NS["rdf"]["resource"] in elem_type.attrib:
+ type_iri = elem_type.attrib[_NS["rdf"]["resource"]]
+ type_ = curies.get(type_iri) or self._compact_id(type_iri)
+ else:
+ type_ = elem_type.text
+
  try:
+ # recover existing synonym on the entity if there's one already
  synonym = next(
  s._data()
  for s in entity.synonyms
  if s.description == elem_target.text
  and s.scope == _SYNONYMS[property]
  )
+ # update synonym type of existing synonym if we got one
+ if type_ is not None:
+ synonym.type = type_
  except StopIteration:
  description = elem_target.get(_NS["rdf"]["resource"], elem_target.text)
  if description is None:
@@ -822,7 +835,7 @@ def _process_axiom(self, elem: etree.Element, curies: Dict[str, str]):
  synonym = SynonymData(
  description,
  scope=_SYNONYMS[property],
- type=type_.text if type_ is not None else None,
+ type=type_,
  )
 
  entity._data().synonyms.add(typing.cast(SynonymData, synonym))

diff --git a/tests/test_parser/test_rdfxml.py b/tests/test_parser/test_rdfxml.py
@@ -449,3 +449,58 @@ def test_relationship_symmetric(self):
  )
  self.assertIn("TST:001", ont.relationships())
  self.assertTrue(ont.get_relationship("TST:001").symmetric)
+
+ def test_existing_synonym_type_extraction(self):
+ ont = self.get_ontology(
+ """
+ <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/chebi.owl"/>
+
+ <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/chebi#BRAND_NAME">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BRAND NAME</rdfs:label>
+ <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
+ </owl:AnnotationProperty>
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_4508">
+ <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cataflam</oboInOwl:hasRelatedSynonym>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CHEBI:4508</oboInOwl:id>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHEBI_4508"/>
+ <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+ <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cataflam</owl:annotatedTarget>
+ <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DrugBank</oboInOwl:hasDbXref>
+ <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/chebi#BRAND_NAME"/>
+ </owl:Axiom>
+ """
+ )
+ syntype, = ont.metadata.synonymtypedefs
+ synonym, = ont["CHEBI:4508"].synonyms
+ self.assertEqual(synonym.scope, "RELATED")
+ self.assertEqual(synonym.type, syntype)
+
+ def test_missing_synonym_type_extraction(self):
+ ont = self.get_ontology(
+ """
+ <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/chebi.owl"/>
+
+ <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/chebi#BRAND_NAME">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BRAND NAME</rdfs:label>
+ <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
+ </owl:AnnotationProperty>
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_4508">
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CHEBI:4508</oboInOwl:id>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHEBI_4508"/>
+ <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+ <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cataflam</owl:annotatedTarget>
+ <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DrugBank</oboInOwl:hasDbXref>
+ <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/chebi#BRAND_NAME"/>
+ </owl:Axiom>
+ """
+ )
+ syntype, = ont.metadata.synonymtypedefs
+ synonym, = ont["CHEBI:4508"].synonyms
+ self.assertEqual(synonym.scope, "RELATED")
+ self.assertEqual(synonym.type, syntype)