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Pathfinder: Implement node-category constraints #830

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tokebe opened this issue Jul 10, 2024 · 2 comments
Closed

Pathfinder: Implement node-category constraints #830

tokebe opened this issue Jul 10, 2024 · 2 comments

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@tokebe
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tokebe commented Jul 10, 2024

Parent Issue: #794

Pathfinder currently supports a specific query format (see #794) but requires that the intermediate node be of category biolink:NamedThing. This needs to be changed such that the query graph unpinned node can be given a different category. The expected behavior when this occurs:

  • BTE will find paths that must have the given category (or descendant categories) as at least one intermediate node
  • BTE's results will only bind intermediate nodes of the given category (or descendants)

The easiest way to implement this is to somehow filter or fill out the templates BTE uses. We could add an attribute to the templateGroups where all pathfinder-type groups specify a list of intermediate node categories they contain. There may be better ways to go about this (pinging @colleenXu for discussion)

As for only binding only intermediate nodes of the given category, when making final results in pathfinder.ts, we can skip any result where the current intermediate node is not equal to or a descendant of the expected category (making use of biolink utilities).

@tokebe
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tokebe commented Jul 10, 2024

Note that work is blocked until we've decided on an approach for how best to handle pinned categories with respect to our templates.

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tokebe commented Jul 16, 2024

Superseded by #832

@tokebe tokebe closed this as completed Jul 16, 2024
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