Additional updates

mira/dkg/construct.py

@@ -464,7 +464,7 @@ def construct(
  property_values="",
  xref_types="", # TODO
  synonym_types=";".join(
- synonym.type or "skos:exactMatch" for synonym in term.synonyms or []
+ synonym.type.curie for synonym in term.synonyms or []
  ),
  )
  for parent in term.parents:
@@ -781,6 +781,16 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  edge.pred for edge in graph.edges if edge.pred.startswith("http")
  )
 
+ clean_edges = (
+ edge
+ for edge in graph.edges
+ if (
+ edge.subject is not None
+ and edge.predicate is not None
+ and edge.object is not None
+ and edge.object.curie not in OBSOLETE
+ )
+ )
  edges.extend(
  (
  edge.sub,
@@ -792,9 +802,8 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
  version or "",
  )
  for edge in tqdm(
- sorted(graph.edges, key=methodcaller("as_tuple")), unit="edge", unit_scale=True
+ sorted(clean_edges, key=methodcaller("as_tuple")), unit="edge", unit_scale=True
  )
- if edge.obj not in OBSOLETE
  )
 
  for sub, obj, pred_label, pred, *_ in edges:
@@ -970,7 +979,7 @@ def get_node_info(term: pyobo.Term, type: EntityType = "class"):
  property_values="",
  xref_types="",
  synonym_types=";".join(
- synonym.type or "skos:exactMatch" for synonym in term.synonyms or []
+ synonym.type.curie for synonym in term.synonyms or []
  ),
  )
 

mira/dkg/construct_registry.py

@@ -9,7 +9,6 @@
 from typing import Optional, Set
 
 import bioregistry
-import bioregistry.app.impl
 import click
 from bioregistry import Manager
 from tqdm import tqdm

mira/dkg/resources/probonto.py

@@ -1,9 +1,12 @@
 import json
 from collections import defaultdict
+from pathlib import Path
 
 import bioontologies
 import rdflib
 
+HERE = Path(__file__).parent.resolve()
+PROBONTO_PATH = HERE.joinpath("probonto.json")
 
 def get_data_properties(rdf_graph: rdflib.Graph, identifier):
  return {
@@ -24,7 +27,10 @@ def get_instances(obo_graph, probonto_identifier: str):
  ]
 
 
-def get_probonto_terms():
+def get_probonto_terms(*, refresh: bool = False):
+ if PROBONTO_PATH.is_file() and not refresh:
+ return json.loads(PROBONTO_PATH.read_text())
+
  obo_graph = (
  bioontologies.get_obograph_by_prefix("probonto")
  .guess("probonto")
@@ -96,7 +102,7 @@ def get_probonto_terms():
 
 def main():
  results = get_probonto_terms()
- with open("probonto.json", "w") as file:
+ with open(PROBONTO_PATH, "w") as file:
  json.dump(results, file, indent=2, ensure_ascii=False)