-
Notifications
You must be signed in to change notification settings - Fork 8
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 more metabolite and reaction annotations #11
Conversation
iYali 4.1.1
- updated model statistics - remove version number from model identifier (iYali) - more detailed information on how to contribute
I've already worked out that my mapping is far from 100% perfect, in fact the following list of metabolites was mapped to wrong MNX IDs and consequently wrong BioCyc, KEGG and BiGG ids. I'll remove the erroneous mapping in a follow-up commit.
|
An instance of this model with the partial BiGG mapping as IDs can be found here: https://github.com/ChristianLieven/Yarrowia_lipolytica_W29-GEM/tree/bigg_ids |
To review this, I've wanted to pass it through a RAVEN I/O cycle, so that the files should look similar. However, I noticed that RAVEN can currently not I/O SBO terms (issue), so that would mean all SBO terms would be automatically left out. |
RAVEN has been able to to I/O of SBO terms since version 2.3.0. Instead of trying to resolve conflicts in this PR, the code has been refactored in RAVEN using yeast-GEM 8.4.2, see PR #29. |
This PR will add more annotation to the two primary model components: Reactions and Metabolites.
For this I did the following:
chem_xref.tsv
andreac_xref.tsv
.This addition will allow users to translate the model to their favourite namespace
on-the-fly
without having to resort to external databases nor with having to create their own complicated mapping tables.This is the first step for us to make the Yarrowia model accessible on the DD-DeCaF platform (https://caffeine.dd-decaf.eu/), since we currently rely on BiGG Identifiers to display a model's fluxes on the maps we provide. However, having an easily accessible cross-mapping may be useful for others too, which is why I wanted to share my work this way :)
Cheers,
Christian
edit by @edkerk:
devel