A few special symbols deserve a particular treatment when computing MNXref or mapping models
Special symbols for chemical:
- BIOMASS - used to tag growth reaction.
- MNXM01 or PMF (Proton Motive Force) - used to distinguish protons that are transported across a membrane from those that are introduced to balance chemical equations (MNXM1).
Special symbols for compartments:
- BOUNDARY - used to tag "external" exchange reactions. As a consequence, reaction with an empty side are forbidden here.
Special symbols for reaction:
- EMPTY - designates reactions that have no-reactants after being mapped to MNXref, typically these correspond to acid-base or some tautomerization reactions.
Special symbols for peptides/genes:
- SPONTANEOUS - used to tag spontaneous reactions. Reactions with no enzymes nor this tag have an unknow or unspecified catalyst.