#110 Defining boundary reactions
In constraint-based models three specific types of reactions are widely used:
1) Exchange reactions (often abbreviated as R_EX_.)
2) Demand Reactions (often abbreviated as R_DM_.)
3) Biomass production (usually marked as R_BIOMASS_.*)
These are usually the only three kinds of reactions that are legally not mass-balanced (see a recent paper here: http://identifiers.org/pubmed/25725218)
About 1) Exchange reactions can operate in the negative (uptake) direction or positive (secretion) direction. However, these are not to be confused with transport reactions. A transport reaction can be linked to an exchange reaction. The purpose of exchange reactions is to provide some sort of influx or efflux of matter to the model. The reactions are "made up" for modeling purposes and do not have a physical correspondence.
About 2) Demand reactions are similar to exchange reactions, but operate on "internal" metabolites. Metabolites that are consumed by these reactions are assumed to be used in intra-cellular processes that are not part of the model. Demand reactions can also deliver metabolites (from intra-cellular processes that are not considered in the model).
About 3) The biomass production is usually the optimization target reaction of constraint-based models. While 1 & 2 usually consume/produce exactly one metabolite, the biomass reaction can have multiple reactants and products. It is assumed that parts of the reactants are also consumed in "omitted processes" and the products do therefore not have to reflect all the atom composition of the reactants.
It would be nice if SBO would provide terms to specifically define and annotate these three kinds of reactions.
Discussion
Anonymous
After discussion with Andreas Dräger and Zak King, created the following terms:
demand reaction: http://identifiers.org/biomodels.sbo/SBO:0000628
exchange reaction: http://identifiers.org/biomodels.sbo/SBO:0000627
ATP maintenance: http://identifiers.org/biomodels.sbo/SBO:0000630
biomass production: http://identifiers.org/biomodels.sbo/SBO:0000629
Thanks for your contribution,
cheers
Nick