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 annotations for KEGG pathways and genes #107

Open
NantiaL opened this issue May 3, 2022 · 1 comment
Open

Add annotations for KEGG pathways and genes #107

NantiaL opened this issue May 3, 2022 · 1 comment
Labels
feature Issues that aim to introduce new feature in ModelPolisher.

Comments

@NantiaL
Copy link

NantiaL commented May 3, 2022

It would be very useful to have annotations for KEGG subsystems and genes assigned by the ModelPolisher. This would save a lot of time and work during model curation.

To obtain genes' annotations one of the following methods could be used:

  • the GenBank file combined with old/new locus tags
  • the NCBI API
  • the KEGG API and the conv operation
@NantiaL NantiaL changed the title Add KEGG pathways and gene annotations Add annotations for KEGG pathways and genes May 3, 2022
@matthiaskoenig
Copy link
Collaborator

Just to comment on this. KEGG is basically dead for many researchers since moving behind a non-open license. This makes it basically impossible to work with KEGG data and annotations. Many researchers dropped KEGG in recent years (as did I). I would not recommend to put any effort in supporting KEGG, but instead use open alternatives such as reactome.

@Schmoho Schmoho added enhancement feature Issues that aim to introduce new feature in ModelPolisher. and removed enhancement labels May 3, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
feature Issues that aim to introduce new feature in ModelPolisher.
Projects
None yet
Development

No branches or pull requests

3 participants