DRUGBANK:drug-interaction is incorrectly being mapped to biolink:physically_interacts_with

[saramsey]

This issue was brought to my attention by NCATSTranslator/Feedback issue 415.

Confirmed, in Neo4j endpoint kg2endpoint-kg2-8-4.rtx.ai, the Cypher query

match (n {id: 'DRUGBANK:DB00393'})-[r]-(m {id: 'DRUGBANK:DB04695'}) return r;

returns the JSON result

{   "predicate": "biolink:physically_interacts_with",   "domain_range_exclusion": "False",   "negated": "False",   "primary_knowledge_source": "infores:drugbank",   "relation_label": "drug_interaction",   "publications_info": "{'sentence': 'The risk or severity of QTc prolongation can be increased when Farnesyl thiopyrophosphate is combined with Nimodipine.'}",   "subject": "DRUGBANK:DB04695",   "source_predicate": "DRUGBANK:drug-interaction",   "predicate_label": "drug-interaction",   "id": "DRUGBANK:DB04695---DRUGBANK:drug-interaction---None---None---None---DRUGBANK:DB00393---identifiers_org_registry:drugbank",   "object": "DRUGBANK:DB00393" }
--
{   "predicate": "biolink:physically_interacts_with",   "domain_range_exclusion": "False",   "negated": "False",   "primary_knowledge_source": "infores:drugbank",   "relation_label": "drug_interaction",   "publications_info": "{'sentence': 'The risk or severity of QTc prolongation can be increased when Farnesyl thiopyrophosphate is combined with Nimodipine.'}",   "subject": "DRUGBANK:DB00393",   "source_predicate": "DRUGBANK:drug-interaction",   "predicate_label": "drug-interaction",   "id": "DRUGBANK:DB00393---DRUGBANK:drug-interaction---None---None---None---DRUGBANK:DB04695---identifiers_org_registry:drugbank",   "object": "DRUGBANK:DB04695" }

which seems like it should not be the correct mapping for a drug interaction.

[saramsey]

So the issue here is that there seems to be no appropriate Biolink predicate to represent this interaction. In the current biolink-model.yaml file, DRUGBANK:interacts-with is mapped to biolink:physically_interacts_with, as shown here: https://github.com/biolink/biolink-model/blob/450cb767f03da6f171b20809dd4a45aed20bb6a4/biolink-model.yaml#L2314-L2341 I agree, biolink:physically_interacts_with is wrong. But so it biolink:genetically_interacts_with. We can't use biolink:interacts_with because it is a mixin. The only other option is biolink:related_to which is rather uninformative. So yes, on one level this is a problem in KG2pre, but on the other hand, we're blocking on clarification from the Biolink team about how to handle this.

[saramsey]

This issue is blocking on biolink/biolink-model issue 1371.