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

Is ARAX-connect.py synonymizing node IDs to the "preferred" CURIEs? #2267

Open
saramsey opened this issue Apr 16, 2024 · 1 comment
Open
Assignees
Labels

Comments

@saramsey
Copy link
Member

In the transition from KG2.8.4c to KG2.9.0c, where the preferred CURIE prefix for chemical substances seemed to switch to UNII, we noticed that the regression test
test_ARAX_connect.py::test_connect_ulcerative_colitis_to_adalimumab failed, and to fix it, we had to change the drug node's CURIE ID from the old ID (DrugCentral:4904) to the new ID (UNII:FYS6T7F842).
df7c8e1#diff-747ec5341c314b256f7d29d7239db0b4dceab85de33259046b1fbb813dfdc8b6

This change made the test pass once again. But from inspecting the ARAX logs, it looks like DrugCentral:4904 is supposed to be synonymized to the preferred CURIE UNII:FYS6T7F842. But it looks like the ARAX connect module isn't using synonymization? Can someone please check? Thanks.

@dkoslicki
Copy link
Member

@mohsenht Can you look into this? In particular, it will definitely be critical to include synonymization in the ARAX connect module. We can follow up via slack or in person to discuss how to implement this.

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

No branches or pull requests

3 participants