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biothings / pending.api

Set of standalone APIs built with the BioThings SDK for the Translator Project
https://biothings.ncats.io
Apache License 2.0
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BioThings FoodData Central parser change #170

Open colleenXu opened 8 months ago

colleenXu commented 8 months ago

I suggest changing the FOODON IDs to be numeric (remove the FOODON_ part of the ID).

Biolink-model folks have told us to use the BioRegistry regex strings for ID-format, and BioRegistry shows that FOODON IDs should be 8-digit numeric. Right now our IDs all start with "FOODON_". We hadn't heard this policy clarification when we were setting up this API and wondering about the ID format.

And something to think on and decide: in ~22% of the dataset, the nutrient wasn't actually found in the food (object.nutrientAmount = 0). I'm not sure if we want to keep this info or not.

It's not an issue for BTE use because I can use the BioThings filter parameter to only retrieve records with amount > 0.

(based on https://github.com/biothings/biothings_explorer/issues/683#issuecomment-1870035991)

colleenXu commented 8 months ago

@everaldorodrigo @newgene

It looks like this issue is being addressed, yay!

If you have decided on keeping/removing the object.nutrientAmount = 0 records, can you add that to this issue?

colleenXu commented 8 months ago

Did we want to keep this issue open until it was deployed on all instances (ncats.io and all ITRB instances transltr.io)?

newgene commented 8 months ago

yes, labelled it as "on CI" for now.