Model organism description

MetabolicAtlas / standard-GEM

The standard for open-source GEMs on GitHub

https://www.biorxiv.org/content/10.1101/2023.03.21.512712

Creative Commons Attribution 4.0 International

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Model organism description #13

Closed Midnighter closed 4 years ago

Midnighter commented 4 years ago

:red_square: Pick a repository description The description must include the taxonomic classification in full. Example: The consensus GEM for Saccharomyces cerevisiae

Maybe this belongs more in a guide on how to construct models but it doesn't hurt to have it in description and model annotation:

A recommendation to use (I suppose) NCBI taxonomy name and ID
The reference genome used to construct the model

mihai-sysbio commented 4 years ago

I believe these 2 fields are meant to be part of the Keywords section in the README. If you don't mind, I'll integrate those two bullet points there.

The repository description refers to the GitHub repository description, see screenshot below:

Just to check, you'd suggest to add the ID and ref genome there?

Midnighter commented 4 years ago

Keywords are a great place, too, although somewhat limited since they don't allow spaces. I think the description is fine as you suggest. Most importantly, all three pieces of information (name, ID, reference genome) should be annotated in SBML.

mihai-sysbio commented 4 years ago

I'm hoping this issue is resolved, please reopen if otherwise.