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MyChem drugcentral bioactivity: write reverse operations #905

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colleenXu opened this issue Dec 12, 2024 · 1 comment
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MyChem drugcentral bioactivity: write reverse operations #905

colleenXu opened this issue Dec 12, 2024 · 1 comment
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@colleenXu
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With BioThings team member's help (thanks @newgene and @ctrl-schaff), it looks like it's possible to write equivalent reverse operations for the MyChem drugcentral bioactivity data.

This would be great, since it would mean we can do the same complex modeling (predicate/qualifier-sets) for subsets of the data based on action_type.

Here's the reverse for activator: NCATS-Tangerine/translator-api-registry@28d8ef5

Note that this doesn't allow batch, since we match on action_type and input ID. Similar idea to #727 (comment), noted in #316 (comment)

@colleenXu
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Done! The commits are from NCATS-Tangerine/translator-api-registry@28d8ef5 to NCATS-Tangerine/translator-api-registry@495ae9b.
This means the drugcentral bioactivity data (complex chem <-> gene relationships) can now be retrieved in both directions with the same complex data-modeling (predicates, qualifiers).

All instances of BTE are currently using the MyChem yaml in the remove-clinical-trials branch - also noted here.
I've updated this branch (merge master which includes these commits). So it'll be live starting Fri 12/20.


But note! The new reverse operations aren't batch-queries because of the logic needed (match a specific gene ID).

Later, because these are not batch queries, maybe we could use the GET method. (Then pagination support could be built to use fetch_all param, but in reality we probably don't need pagination for this data).

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