update predicate mapping to refer to qualified predicates for regulates

biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology

https://biolink.github.io/biolink-model/

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update predicate mapping to refer to qualified predicates for regulates #1491

Open sierra-moxon opened 2 months ago

sierra-moxon commented 2 months ago

fixes https://github.com/NCATSTranslator/Feedback/issues/744 outstanding questions for discussion at DM call:

Should “object_aspect_qualifier=’activity_or_abundance’” be required?
Should “object_direction_qualifier=’downregulated’” or “object_direction_qualifier=’upregulated’” be required?
New associations help define these requirements, what does process regulates process association look like in light of the discussion above.

mikebada commented 2 months ago

For assertions of regulation (not upregulation/downregulation), the qualified predicate causes shouldn't be used (correct?), in which case the qualified predicate shouldn't be required, correct?

sierra-moxon commented 2 months ago

@mikebada - I wrote down in the notes that we wanted there to always be an aspect qualifier because we wanted folks to be able to search for activity or abundance qualifier and get back regulates? But then I got into a bit of a circle with causes activity or abundance.... (without a direction)

mikebada commented 2 months ago

OK, for regulation (not upregulation/downregulation), if we want there to be an aspect (specifically, activity or abundance), then I think that would require affects as the qualified predicate. So, can we say that the allowed values for the qualified predicate for this association type are either affects (for regulation) or causes (for upregulation/downregulation)?