Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add PharmGKB mappings for genes, diseases, variants, and chemicals #171

Open
andrewsu opened this issue Mar 8, 2023 · 1 comment
Open
Labels
Babel Issue applies to babel.

Comments

@andrewsu
Copy link

andrewsu commented Mar 8, 2023

To incorporate the PharmGKB API as described in biothings/biothings_explorer#556, we need node normalizer to resolve PharmGKB identifiers for genes, diseases, variants, and chemicals. Examples of each:

Gene: BRAF - https://www.pharmgkb.org/gene/PA25408
Disease: leukemia - https://www.pharmgkb.org/disease/PA444750
Variant: rs113488022 - https://www.pharmgkb.org/variant/PA166157522
Chemical: imatinib - https://www.pharmgkb.org/chemical/PA10804

Mappings can be found in the "Primary Data" section of https://www.pharmgkb.org/downloads

Related issue to add prefixes to biolink model: biolink/biolink-model#1236

@andrewsu
Copy link
Author

Note that the prefixes have now been added to Biolink model in biolink/biolink-model#1236, which was probably a prerequisite for this issue.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Babel Issue applies to babel.
Projects
None yet
Development

No branches or pull requests

2 participants