Closed miquelduranfrigola closed 1 year ago
We have decided to pause the API for the moment and focus on enriching the backend in the KG with more edges.
For the future, the API we are working in is of the following type:
from pgxembeddings import Chemical
ch = Chemical()
ch.name = "izoniazid"
print(ch.get_associated_variants())
There is work in progress on the PharmGKB side to develop an API (not completed yet) I'll close this issue as the api is already good enough as is: https://api.pharmgkb.org/
We need to write a simple Python API to access PharmGKB on a static (downloaded) form.
Ideally, we want to mirror the PharmGKB interface organization, which is very nicely structured.
We will have different types of entities, namely
Chemical
,Gene
,Variant
,Haplotype
andDisease
See incipient code here: https://github.com/ersilia-os/pharmacogx-embeddings/blob/main/src/pharmgkb.py