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

Unexpected: Neomycin isn't the main name for its clique #382

Open
colleenXu opened this issue Dec 28, 2024 · 1 comment
Open

Unexpected: Neomycin isn't the main name for its clique #382

colleenXu opened this issue Dec 28, 2024 · 1 comment

Comments

@colleenXu
Copy link

I was looking up an ID for neomycin, and the main label for the clique was Framycetin. It looks like Framycetin (aka neomycin B) is a component of the better-known neomycin.

@gaurav gaurav added this to the Issues needing investigation milestone Dec 31, 2024
@gaurav
Copy link
Collaborator

gaurav commented Dec 31, 2024

Thanks for reporting this! The problem is that all the sources we trust most for chemicals (DrugBank, DrugCentral and CHEBI) return both "neomycin" and "Framycetin" (for different identifiers) as the label for this chemical. So I'm not sure how to prefer "neomycin" for this clique. Some options:

  1. Choose the numerically smallest identifier suffix (but that won't work in this case, since Framycetin has the smaller DrugBank identifier suffix).
  2. Choose the shortest label among the most preferred source ("neomycin" is shorter by one character).
  3. Get rid of the chemical preferred name system, and go with the label of the first identifier (in this case, that would give us Neomycin, since it has the lower identifier suffix for CHEBI). We might be able to do that, since Biolink now prefers better names in its prefix order for chemicals anyway.

I'll see if I can come up with some sort of tool we can use to compare different chemical identifier strategies.

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