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standard-GEM: standardization of open-source genome-scale metabolic models

Anton, M.; Almaas, E.; Benfeitas, R.; Benito-Vaquerizo, S.; Blank, L. M.; Dräger, A.; Hancock, J. M.; Kittikunapong, C.; König, M.; Li, F.; Liebal, U. W.; Lu, H.; Ma, H.; Mahadevan, R.; Mardinoglu, A.; Nielsen, J.; Nogales, J.; Pagni, M.; Papin, J. A.; Patil, K. R.; Price, N. D.; Robinson, J. L.; Sanchez, B. J.; Suarez Diez, M.; Sulheim, S.; Svensson, L. T.; Teusink, B.; Vongsangnak, W.; Wang, H.; Zeidan, A. A.; Kerkhoven, E. J.

2023-03-23 systems biology
10.1101/2023.03.21.512712 bioRxiv
Show abstract

The field of metabolic modelling at the genomescale continues to grow with more models being created and curated. This comes with an increasing demand for adopting common principles regarding transparency and versioning, in addition to standardisation efforts regarding file formats, annotation and testing. Here, we present a standardised template for git-based and GitHub-hosted genome-scale metabolic models (GEMs) supporting both new models and curated ones, following FAIR principles (findability, accessibility, interoperability, and reusability), and incorporating bestpractices. standard-GEM facilitates the reuse of GEMs across web services and platforms in the metabolic modelling field and enables automatic validation of GEMs. The use of this template for new models, and its adoption for existing ones, paves the way for increasing model quality, openness, and accessibility with minimal effort. Availabilitystandard-GEM is available from github.com/MetabolicAtlas/standard-GEM under the conditions of the CC BY 4.0 licence along with additional supporting material.

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