#113 Subsystem of reactions
In COBRA models, reactions can be taged with an optional attribute "subsystem", which is comparable to pathway or submodel/submodule of a genome-scale model, or simply a group of reactions, such as all transport reactions within a model. Such subsystems can be represented in SBML by adding these reactions as members to groups (using the groups package with group kind partonomy).
It would be desirable to have a specific SBO term that allows users to distinguish subsystem groups from other groups. The explaining text could say that this is a widely used expression in COBRA models and only refers to reactions, but implicitly also includes all reaction participants (such as metabolites, i.e., substrates and products as well as modifiers and genes that encode for catalyzing enzymes).
This SBO term would help to indicate that such groups of reactions should interprete the members as a whole, i.e., not only the reaction object itselve, but also all of its participants. Here, participants are not only references to species etc., but the species themselves that are for numerous reasons not included in these subsystems.
For more information, please see the discussion here: https://github.com/opencobra/cobrapy/pull/229#issuecomment-191970174
Discussion
Anonymous
Please review the description and feel free to suggest improvements: identifiers.org/biomodels.sbo/SBO:0000633
cheers
Nick