Missing data in v3 API compared to v1?

monarch-initiative / monarch-app

Monarch Initiative website and API

https://monarchinitiative.org/

BSD 3-Clause "New" or "Revised" License

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Missing data in v3 API compared to v1? #577

Closed colleenXu closed 9 months ago

colleenXu commented 9 months ago

I couldn't find the following kinds of data in the current API when searching by association-type.

Disease ⭤ Pathway (example)
any relationship with Variants (dbSNP/rsIDs): there used to be Disease ⭤ Variant, Gene ⭤ Variant, Phenotype ⭤ Variant
gene ortholog ⭤ Disease
gene ortholog ⭤ Phenotype

Are they no longer available though this API?

(CC @kevinschaper, related to https://github.com/biothings/biothings_explorer/issues/774)

kevinschaper commented 9 months ago

We don't currently have disease to pathway or any variant data.

Right now the endpoint is a fairly direct representation of the kgx with necessary ontology closure info for indirect lookups, so we're not providing the two hop gene to disease or gene to phenotype via orthology as associations. We do plan to support that again eventually, but haven't yet settled on how.

colleenXu commented 9 months ago

Question answered, so I'm closing the issue...

colleenXu commented 9 months ago

@kevinschaper Ooops, I just remembered. I also see no items for a specific association-type: Chem to Disease/Pheno.

Is that expected?