Add additional info to docstring, adjust node properties and relation…

… info

mira/dkg/construct.py

@@ -434,6 +434,14 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
  under the corresponding entry's subtree in its respective ontology.
  Relation information is also extracted with this option.
 
+ Running this method for the first time for each specific resource will
+ take a long time (minutes) as the obo resource file has to be downloaded,
+ converted to a networkx graph, have their node indices normalized, and
+ pickled.
+
+ Subsequent runs of this method will take a few seconds as the pickled
+ graph object has to be loaded.
+
  Parameters
  ----------
  curie :
@@ -479,6 +487,10 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
  if not node:
  return nodes, edges
  if not add_subtree:
+ property_dict = defaultdict(list)
+ for text in node.get("property_value", []):
+ k, v = text.split(" ", 1)
+ property_dict[k].append(v)
  nodes.append(
  {
  "id": curie,
@@ -494,15 +506,18 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
  "alts": [],
  "xrefs": [Xref(id=xref_curie.lower(), type="")
  for xref_curie in node["xref"]],
- "properties": {k: v for text in node[
- "property_value"] for k, v in [text.split(" ")]}
+ "properties": property_dict
  }
  )
  return nodes, edges
  else:
  for node_curie in networkx.ancestors(relabeled_graph, curie) | {curie}:
  node_curie = node_curie
  node = relabeled_graph.nodes[node_curie]
+ property_dict = defaultdict(list)
+ for text in node.get("property_value", []):
+ k, v = text.split(" ",1)
+ property_dict[k].append(v)
  nodes.append(
  {
  "id": node_curie,
@@ -518,8 +533,7 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
  "alts": [],
  "xrefs": [Xref(id=xref_curie.lower(), type="")
  for xref_curie in node.get("xref", [])],
- "properties": {k: v for text in node.get(
- "property_value", []) for k, v in [text.split(" ")]}
+ "properties": property_dict
  }
  )
  # Don't add relations where the original curie to add is the source
@@ -529,8 +543,8 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
  edges.append(
  {
  "source_curie": node_curie,
- "target_curie": node["is_a"][0],
- "type": is_a.name,
+ "target_curie": node["is_a"][0].lower(),
+ "type": is_a.name.replace(" ","_"),
  "pred": is_a.curie,
  "source": resource_prefix,
  "graph": resource_prefix,