Process the GEMs from Wang et al., 2021 (https://github.com/SysBioChalmers) into convenient tables.
Arguments
- organism
Character or integer: an organism (taxon) identifier. Supported taxons are 9606 (Homo sapiens), 10090 (Mus musculus), 10116 (Rattus norvegicus), 7955 (Danio rerio), 7227 (Drosophila melanogaster) and 6239 (Caenorhabditis elegans).
- orphans
Logical: include orphan reactions (reactions without known enzyme).
Value
List containing the following elements:
reactions: tibble of reaction data;
metabolites: tibble of metabolite data;
reaction_ids: translation table of reaction identifiers;
metabolite_ids: translation table of metabolite identifiers;
S: Stoichiometric matrix (sparse).
References
Wang H, Robinson JL, Kocabas P, Gustafsson J, Anton M, Cholley PE, Huang S, Gobom J, Svensson T, Uhlen M, Zetterberg H, Nielsen J. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):e2102344118. doi: doi:10.1073/pnas.2102344118 .