how to keep metanetx_universal_model_bigg_rhea_kegg_brenda database updated with metanetx database

biosustain / cameo

cameo - computer aided metabolic engineering & optimization

http://cameo.bio

Apache License 2.0

114 stars 44 forks source link

how to keep metanetx_universal_model_bigg_rhea_kegg_brenda database updated with metanetx database #204

Open chang88ye opened 6 years ago

chang88ye commented 6 years ago

Some metanetx reaction or metabolite identifiers keep being depreciated. How do I update metanetx_universal_model_bigg_rhea_kegg_brenda accordingly ?

phantomas1234 commented 6 years ago

Thanks for letting us know, we'll upgrade the universal models in an upcoming release (reopening this issue so that we don't forget). Of course, contributions in the form of pull requests are always welcome (the script that creates the universal models can be found here https://github.com/biosustain/cameo/blob/devel/scripts/parse_metanetx.py).

sruti-dammalapati commented 2 years ago

Wondering if someone has worked on this? If not, I've made some updates to the parser to build the latest models from metanetx. There were many identifiers that deprecated over the last five years. I will be happy to submit a pull request!

phantomas1234 commented 2 years ago

@sruti-dammalapati thanks, that would be great!