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biothings / biothings_explorer

TRAPI service for BioThings Explorer
https://api.bte.ncats.io
Apache License 2.0
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ID/Node-expansion for UMLS IDs: analyzing and fixing #518

Open colleenXu opened 1 year ago

colleenXu commented 1 year ago

In the ID/Node-expansion first attempt https://github.com/biothings/bte_trapi_query_graph_handler/pull/113, we note that UMLS descendant retrieval seems odd (overview in a bullet-point of this post, details in top section of this post, original post on umls support here).

Involves digging into what the node-expansion package https://github.com/biothings/node-expansion is doing with UMLS IDs.

This issue was first identified for "chemicals" but it's not clear how widespread this issue is. Some diseases seemed to have fine responses...

colleenXu commented 8 months ago

Another example: For the SmallMolecule Fluconazole (UMLS:C0016277), the node-expansion module is returning ClinicalAttributes as descendants, like:

colleenXu commented 3 months ago

Potentially useful info: my digging into what node-expansion is using and what UMLS Metathesaurus is saying https://github.com/biothings/biothings_explorer/issues/792#issuecomment-2033121295