Table 3.

Kinds of species that can potentially act as enzymes and their top-level SBO terms. In the preprocessing step (see Algorithm 3 in Additional file 2), the algorithm for the de novo creation of kinetic equations categorizes reaction modifiers into four different groups: enzymes E, activators and stimulators A, inhibitors I, and non-enzyme catalysts C. To this end, it first analyzes the SBO term assigned to the modifier itself (see Table 2). It then obtains the actual species that acts as a modifier in the current reaction and analyzes this species’ SBO terms, assuming that this annotation defines the material classes of the species. The SBO terms in this table represent the top-level terms, i.e., the algorithm also accepts each more specialized term for a specific category. Note that the user can exclude elements from this list and therefore influence the algorithm’s choices. If the material class of a modifier’s species falls into one of the allowable SBO categories, the algorithm will categorize this modifier as an enzyme and potential contradictions with the modifier’s SBO term will be resolved

Material entity	SBO term
Antisense RNA (asRNA)	SBO:0000317
Complex	SBO:0000253
Generic protein	SBO:0000252
Macromolecule	SBO:0000245
Receptor	SBO:0000244
RNA	SBO:0000250
Simple molecule	SBO:0000247
Truncated protein	SBO:0000248
Unknown molecule	SBO:0000285