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

Variant page - New somatic quick links #992

Open
davmlaw opened this issue Feb 15, 2024 · 3 comments
Open

Variant page - New somatic quick links #992

davmlaw opened this issue Feb 15, 2024 · 3 comments

Comments

@davmlaw
Copy link
Contributor

davmlaw commented Feb 15, 2024

Maybe do #758 first/same time

Anna B suggested:

  • Cancer hotspots
  • Onco KB (already there but not as quick links)
  • Cancer bio (confirm link?)
@davmlaw davmlaw added this to the SA Path VG 4 milestone Feb 15, 2024
@TheMadBug
Copy link
Member

So if you look at how QuickLinks works, we provide certain evidence keys to vc_links.js. When showing quick links, we only pass:
variant coordinate
variant string - as in str(variant)
genome build
canonical c.HGVS

There's a few keys that we have at the allele level that we don't currently pass:
clingen_allele_id,

We don't pass gene symbol, as it's not something directly on the allele, though we could extract it from the canonical c.HGVS

Passing the gene_symbol to quick links should just enable OncoKB. Alternatively maybe we put a list of gene symbol quick links separate from the per variant quick links?

Note that quick links was developed as one of the first things of variant classifications, and have sat theere relatively untouched ever since.

@davmlaw
Copy link
Contributor Author

davmlaw commented May 14, 2024

We now have gene level quick links on the gene symbol page - which lets you click the onco KB, you need to click to expand

The other stuff doesn't have a way to do gene specific landing

@davmlaw davmlaw closed this as completed Aug 18, 2024
@EmmaTudini
Copy link
Contributor

Re-opening to see whether this makes it into Shariant test on the next deploy

@EmmaTudini EmmaTudini reopened this Aug 23, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

3 participants