Table 2 SBO terms with relevance for the categorization of reactions. The preprocessing algorithm (see Algorithm 3 in Additional file 2) uses the SBO terms listed in this table in order to distinguish between different types of species and modification in order to categorize a each reaction in the submodel as well as the role of individual reaction participants. This also includes further relevant material entities of reaction participants. Note that the algorithm always checks if the SBO term of an element is a child of a certain reference term in order to also include all more specific sub-terms
From: SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
Definition | SBO term |
|---|---|
Catalyst | SBO:0000013 |
Empty set | SBO:0000291 |
Enzymatic catalyst | SBO:0000460 |
Gene | SBO:0000243 |
Gene-coding region | SBO:0000335 |
Generic | SBO:0000252 |
Inhibition | SBO:0000169 |
Inhibitor | SBO:0000020 |
MRNA | SBO:0000278 |
Necessary stimulation | SBO:0000171 |
Protein | SBO:0000297 |
RNA | SBO:0000250 |
Stimulation | SBO:0000170 |
Stimulator | SBO:0000021 |
Transcriptional activation | SBO:0000459 |
Transcriptional inhibition | SBO:0000020 |
Translational activation | SBO:0000459 |
Trigger (necessary stimulator) | SBO:0000461 |
Translation | SBO:0000184 |
Transcription | SBO:0000183 |