Table 2 BioPAX instances and ontology terms corresponding to KGML relation subtypes
From: Precise generation of systems biology models from KEGG pathways
Relation subtype | BioPAX element | SBO term | MI term | GO term |
|---|---|---|---|---|
activation | conversion, control | 170 (stimulation) | none | none |
inhibition | conversion, control | 169 (inhibition) | none | none |
expression | TemplateReaction, -Regulation | 170 (stimulation) | none | 10467 |
repression | TemplateReaction, -Regulation | 169 (inhibition) | none | none |
indirect effect | conversion | 344 (molecular interaction) | none | none |
state change | conversion | 168 (control) | none | none |
binding/association | ComplexAssembly | 177 (non-covalent binding) | 914 | 5488 |
dissociation | ComplexAssembly | 180 (dissociation) | none | none |
missing interaction | MolecularInteraction | 396 (uncertain process) | none | none |
phosphorylation | conversion, control | 216 (phosphorylation) | 217 | 16310 |
dephosphorylation | conversion, control | 330 (dephosphorylation) | 203 | 16311 |
glycosylation | conversion, control | 217 (glycosylation) | 559 | 70085 |
ubiquitination | conversion, control | 224 (ubiquitination) | 220 | 16567 |
methylation | conversion, control | 214 (methylation) | 213 | 32259 |