Final updates

gyorilab · Jul 5, 2023 · 7da8322 · 7da8322
1 parent 61edaaa
commit 7da8322
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Showing 2 changed files with 15 additions and 10 deletions.
diff --git a/mira/dkg/construct.py b/mira/dkg/construct.py
@@ -564,8 +564,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  f"{manager.get_name(prefix)} ({len(_graphs)} graphs)", fg="green", bold=True
  )
  for graph in tqdm(_graphs, unit="graph", desc=prefix, leave=False):
- if not graph.id:
- raise ValueError(f"graph in {prefix} missing an ID")
+ graph_id = graph.id or prefix
  version = graph.version
  if version == "imports":
  version = None
@@ -623,7 +622,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  .replace(" ", " ")
  if node.name
  else "",
- synonyms=";".join(synonym.val for synonym in node.synonyms),
+ synonyms=";".join(synonym.value for synonym in node.synonyms),
  deprecated="true" if node.deprecated else "false", # type:ignore
  # TODO better way to infer type based on hierarchy
  # (e.g., if rdfs:type available, consider as instance)
@@ -639,7 +638,8 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  property_values=";".join(property_values),
  xref_types=";".join(xref_predicates),
  synonym_types=";".join(
- synonym.pred for synonym in node.synonyms
+ synonym.predicate.curie if synonym.predicate else synonym.predicate_raw
+ for synonym in node.synonyms
  ),
  )
 
@@ -651,7 +651,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  "replaced_by",
  "iao:0100001",
  prefix,
- graph.id,
+ graph_id,
  version or "",
  )
  )
@@ -690,7 +690,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  "xref",
  "oboinowl:hasDbXref",
  prefix,
- graph.id,
+ graph_id,
  version or "",
  )
  )
@@ -713,12 +713,15 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  synonym_types="",
  )
 
- for provenance_curie in node.get_provenance():
+ for provenance in node.get_provenance():
+ if ":" in provenance.identifier:
+ tqdm.write(f"Malformed provenance for {node.curie}")
+ provenance_curie = provenance.curie
  node_sources[provenance_curie].add(prefix)
  if provenance_curie not in nodes:
  nodes[provenance_curie] = NodeInfo(
  curie=provenance_curie,
- prefix=provenance_curie.split(":")[0],
+ prefix=provenance.prefix,
  label="",
  synonyms="",
  deprecated="false",
@@ -739,7 +742,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  "has_citation",
  "debio:0000029",
  prefix,
- graph.id,
+ graph_id,
  version or "",
  )
  )
@@ -785,7 +788,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  _get_edge_name(edge.pred).lower().replace(" ", "_").replace("-", "_"),
  edge.pred,
  prefix,
- graph.id,
+ graph_id,
  version or "",
  )
  for edge in tqdm(

diff --git a/mira/dkg/construct_rdf.py b/mira/dkg/construct_rdf.py
@@ -27,6 +27,8 @@
  # Should be fixed in https://github.com/geneontology/go-ontology/pull/24148
  # and after HP re-imports GO
  "doi:10.1002/(SICI)1097-4687(199608)229:2<121::AID-JMOR1>3.0.CO;2-4",
+ # https://github.com/obophenotype/human-phenotype-ontology/pull/9812
+ "pubmed:14645606|PMID:14647932|PMID:31669363",
 }
 REMAPPING = {
  REFERENCED_BY_SYMBOL: "debio:0000030",