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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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GeneAffectsChemicalAssociation with qualifiers #1387

Closed RichardBruskiewich closed 1 year ago

RichardBruskiewich commented 1 year ago

Problem: The current Biolink Model has a ChemicalAffectsGeneAssociation, but doesn't have a GeneAffectsChemicalAssociation. Some KPs have a significant number of edges of the latter format, but is unsuccessfully attempting to annotate those edges with qualifiers (and qualifier value ranges) only defined in the former association class. This leads validation errors (as of reasoner-validator 3.8.8 validating against Biolink Model 3.5.4).

Example:

This legitimate edge does not validate:

subject: TRPC4 predicate: affects object: Barium object_aspect_qualifier: transport object_direction_qualifier: increased

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

Describe the solution you'd like

Add GeneAffectsChemicalAssociation class annotated with suitable qualifiers and qualifier value ranges/subproperties. A simple search for the inverse association won't necessarily work since the inverse predicate is affected_by not affects.

Tag relevant members for discussion @sierra-moxon @mbrush @vdancik

RichardBruskiewich commented 1 year ago

Resolved by PR https://github.com/biolink/biolink-model/pull/1388