Principles for catalytic activity terms

NAD/NADP cofactors

• Reactions represented with NAD(P) in GO indicates that it is not know whether an enzyme uses NAD or NADP (note that this is different from the IUBMB practice).
  • If the cofactor (NAD or NADP) is unknown for a class of reactions, then we only create a single GO term with [NAD(P)].
    • If there are RHEA IDs for both NAD and NADP-dependent reactions, we add these as NARROW xref to the general [NAD(P)].

• If the specific cofactor is known, we create one or both relevant reactions. In this case, we also create (or keep= a general parent grouping class with [NAD(P)]. The structure of the ontology is:

           x activity NAD(P)
               x activity NAD
               x activity NADP

• • If an enzyme uses both, then it is annotated to both NAD and NADP terms.
  • If the cofactor specificity is always known, then we marke the grouping class 'do not annotate'. An example of this is isocitrate dehydrogenase activity.