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Update loadDrugMechDB.py to include treats edges for indication paths #264

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Update loadDrugMechDB.py to include treats edges for indication paths #264

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3572e34
Update loadDrugMechDB.py to include treats edges for indication paths
beasleyjonm Oct 25, 2024
f5eeb7b
Changed edge between drug and disease to "treats_or_applied_or_studie…
beasleyjonm Dec 11, 2024
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26 changes: 25 additions & 1 deletion parsers/drugmechdb/src/loadDrugMechDB.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,31 @@ def parse_data(self) -> dict:
drug_drugbank = entry["graph"]["drugbank"]
disease_name = entry["graph"]["disease"]
disease_mesh = entry["graph"]["disease_mesh"]
links = entry["links"]
links = entry["links"]

### Add "biolink:treats_or_applied_or_studied_to_treat" edges between the drug and disease in each indication path.
source_target_pair_dict["dmdb_ids"].append(dmdb_id)

source = drug_drugbank
fixed_source = self.fix_node(source,node_mapping)
source_target_pair_dict["source_ids"].append(fixed_source)
output_node = kgxnode(fixed_source)
self.output_file_writer.write_kgx_node(output_node)

target = disease_mesh
fixed_target = self.fix_node(target,node_mapping)
source_target_pair_dict["target_ids"].append(fixed_target)
output_node = kgxnode(fixed_target)
self.output_file_writer.write_kgx_node(output_node)

source_target_pair_dict["qualified_predicates"].append("")
source_target_pair_dict["object_direction_qualifiers"].append("")
source_target_pair_dict["object_aspect_qualifiers"].append("")

predicate = "biolink:treats_or_applied_or_studied_to_treat"
source_target_pair_dict["predicates"].append(predicate)

### Add all explicitly described links in indication path.
for i in range(len(links)):
triple = links[i]

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