Adjust node property attributes

mira/dkg/client.py

@@ -354,7 +354,7 @@ def add_node(self, entity):
  xref_types.append(xref.type)
  for synonym in entity.synonyms:
  synonyms.append(synonym.value)
- synonym_types.append(synonym.value)
+ synonym_types.append(synonym.type)
  for property_predicate, property_value_list in entity.properties.items():
  property_predicates.append(property_predicate)
  property_values.extend(property_value_list)

mira/dkg/construct.py

@@ -218,9 +218,9 @@ def extract_nodes_edges_from_pyobo_terms(term_getter, resource_prefix):
  "type": entity_type,
  "description": term.definition if term.definition else "",
  "obsolete": False if not term.is_obsolete else True,
- "synonyms": [Synonym(value=syn._fp(),
+ "synonyms": [Synonym(value=syn.name,
  type=f"{syn.type.reference.prefix}:"
- f"{syn.type.reference.prefix}")
+ f"{syn.type.reference.identifier}")
  for syn in term.synonyms],
  "alts": term.alt_ids,
  "xrefs": [Xref(value=value, type=type) for value, type in

mira/dkg/resources/cso.py

@@ -23,7 +23,7 @@ def get_cso_obo() -> Obo:
  )
  download(url=URL, path=PATH)
  # use https://github.com/pyobo/pyobo/pull/159
- return from_obo_path(PATH, prefix="cso", default_prefix="cso", strict=False)
+ return from_obo_path(PATH, prefix="cso", strict=False)
 
 
 if __name__ == "__main__":