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

A.0_RHOBTB2_direct.json no results from ARAX #1698

Closed
edeutsch opened this issue Oct 8, 2021 · 2 comments
Closed

A.0_RHOBTB2_direct.json no results from ARAX #1698

edeutsch opened this issue Oct 8, 2021 · 2 comments
Assignees

Comments

@edeutsch
Copy link
Collaborator

edeutsch commented Oct 8, 2021

This one was assigned to me in minihackathons:
NCATSTranslator/minihackathons#323
It looks like we just don't have the data.
I vaguely recall some discussion about including LINC (which does)?

Does anyone know any more about this issue? And can respond? Or otherwise take it from here?
Thanks!

@saramsey
Copy link
Member

saramsey commented Oct 9, 2021

Apparently LINCS Data Portal has been turned into a KP, at least according to Smart API.

Screen Shot 2021-10-08 at 5 08 21 PM

Could be added into Expand perhaps, though I'm not sure if this KP accepts TRAPI queries (its SmartAPI entry is not annotated with TRAPI).

@saramsey
Copy link
Member

I looked into the LINCS data portal at some point, and found that we couldn't really get what we want (which is effects of drugs on cell line gene expression). The stuff that you can get through the LINCS API seems to be already available in sources that we already ETL. For example, the LINCS API says that they get "drug indication" information from EFO (which we already ETL), and drug "bioactivities" from ChEMBL (which we already ETL). I think it is better to just get this information (if we are not already getting it) from those sources that we already ETL rather than get it from LINCS.

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

No branches or pull requests

2 participants