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

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merged 8 commits into from
Sep 23, 2024

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sierra-moxon
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@sierra-moxon sierra-moxon commented Apr 16, 2024

fixes NCATSTranslator/Feedback#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.

@sierra-moxon sierra-moxon requested review from mbrush and mikebada April 16, 2024 03:43
@sierra-moxon sierra-moxon requested a review from vdancik April 16, 2024 04:18
@mikebada
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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?

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sierra-moxon commented Apr 18, 2024

@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)

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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)?

@sierra-moxon sierra-moxon merged commit 03914a7 into master Sep 23, 2024
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Incomplete population of qualifier patterns in qualified edges leads to incorrect composed edge labels
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