Fix-amino acid pathways localization

SysBioChalmers / yeast-GEM

The consensus GEM for Saccharomyces cerevisiae

http://sysbiochalmers.github.io/yeast-GEM/

Creative Commons Attribution 4.0 International

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Fix-amino acid pathways localization #294

Open feiranl opened 2 years ago

feiranl commented 2 years ago

Description of the issue:

Some reactions in amino acid pathways do not reflect the correct compartments

I hereby confirm that I have:

[ ] Tested my code with all requirements for running the model
[ ] Done this analysis in the main branch of the repository
[ ] Checked that a similar issue does not exist already
[ ] If needed, asked first in the Gitter chat room about the issue

hongzhonglu commented 2 years ago

For this issue, I suggest the protein compartment annotation from SGD (https://www.yeastgenome.org/) is used. In general, the protein compartment in the yeast-GEM should be curated in detail besides amino acid pathways localisation. It will be nice to use the same standard in the protein compartment annotation.