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biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/
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DRUGBANK:drug-interaction shouldn't be mapped to biolink:physically_interacts_with #1371

Open saramsey opened 1 year ago

saramsey commented 1 year ago

Describe the bug The biolink-model.yaml file is currently recommending that the source relation DRUGBANK:drug-interaction should be mapped to the predicate biolink:physically_interacts_with. These seem rather semantically inequivalent.

To Reproduce See the permalink here: https://github.com/biolink/biolink-model/blob/450cb767f03da6f171b20809dd4a45aed20bb6a4/biolink-model.yaml#L2314-L2341

We can't use biolink:interacts_with because it is a mixin. The only other option is biolink:related_to which is rather uninformative. Can we have some kind of predicate like biolink:physiologic_interaction or similar?

Expected behavior n/a

What working group (or team) did this request originate from? Results based on this mapping have been reported as a Translator bug, in NCATSTranslator/Feedback issue 415 and this is being tracked in RTXteam/RTX-KG2 issue 340.

Note: This is relevant for members of NCATS Translator.

Additional context We view this issue as fairly high priority due to the upcoming Aug. 18 freeze in advance of the Translator presentation.

Tag relevant members for discussion @sierra-moxon

saramsey commented 10 months ago

Hi Biolink team, just checking back on the status of this issue?

nlharris commented 9 months ago

Hey @saramsey, @sierra-moxon is working on this and there should be movement on it soon!