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Exposing relationship type in GO function queries #138

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cmungall opened this issue Feb 20, 2018 · 3 comments
Open

Exposing relationship type in GO function queries #138

cmungall opened this issue Feb 20, 2018 · 3 comments
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@cmungall
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For querying a gene by go term, we want to allow people to distinguish

  • genes involved in pathway
  • genes regulating pathway

As well as additional forthcoming relationship types

More generally, this would be useful for other kinds of associations too. For gene expression: genes expressed in X or part-of X vs X or part-of X or develops-from X.

Ideally this would be very generic and metadata driven but for now we can just hardcode in the lightweight swagger layer in bioentity.py. This would basically inject something via fq instead of using object.

@selewis requires this for her pathway analysis.

cc @kltm as we need parallel amigo functionality

cc @vanaukenk

Related:
geneontology/amigo#201
cmungall added a commit to geneontology/amigo that referenced this issue Feb 20, 2018
@cmungall
Update ann-config.yaml
7a7bd84 
Clarified semantics of regulates closure and adding a proposed new closure for getting 'regulates only'; i.e. following is_a and regulates (and -/+), with at least one regulates hop in there.

We will want to expose this on amigo, and also via APIs, see monarch-initiative/biolink-api#138

cc @selewis
@cmungall cmungall mentioned this issue Feb 20, 2018
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@cmungall
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To get regulates-only for now, do a subtraction (regulatesClosure MINUS isaPartOfClosure), until we have geneontology/amigo#469

@deepakunni3 deepakunni3 mentioned this issue Mar 5, 2018
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@deepakunni3
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Keeping this issue open to revisit in the future after geneontology/amigo#469 has been implemented.

@selewis
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selewis commented Mar 8, 2018

Super, I'll try it out for Hippo signaling.

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@cmungall @selewis @deepakunni3