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biolink / biolink-model-toolkit

A collection of useful python functions for looking up information and working with the Biolink Model
https://biolink.github.io/biolink-model-toolkit/
BSD 3-Clause "New" or "Revised" License
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Enhance S-P-O pattern matching to biolink:Association subclasses #146

Closed RichardBruskiewich closed 1 month ago

RichardBruskiewich commented 11 months ago

Motivating issue is briefly documented in https://github.com/NCATSTranslator/reasoner-validator/issues/93. See also the related Biolink Model issue.

What working group (or team) did this request originate from?

Aragorn KP (Max Wang)

Solution we'd like

Biolink Model subject--predicate->object ("S-P-O") statements of the form biolink:Gene -- biolink:affects -> biolink:ChemicalEntity may not directly match any available subclass of biolink:Association. That said, it may be feasible to match an 'inverse' S-P-O pattern to a specific subclass of biolink:Association. That is, to transform the above pattern into a meaningful inverse on - for the above example, the pattern biolink:ChemicalEntity -- biolink:affected_by -> biolink:Gene - then reattempt the match.

Tag relevant members for discussion @sierra-moxon

RichardBruskiewich commented 11 months ago

Most of the BMT machinery required to satisfy this issue implemented in PR #143