Table 2

BioPAX instances and ontology terms corresponding to KGML relation subtypes
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

This table shows how relations are handled during conversion to BioPAX or SBML. The conversion depends on the subtype of each relation. For each subtype, the corresponding BioPAX element, as well as terms from different ontologies are specified. When converting to BioPAX, all terms are annotated as an instance of InteractionVocabulary, whereas an SBML transition has a field for the SBO term and other terms are added as controlled vocabularies on the transition. Please note that some BioPAX elements are subject to certain conditions and others need to be replaced by more generic classes in BioPAX Level 2, due to differences in both releases. Please see the KEGG to BioPAX section for more details.

Wrzodek et al.

Wrzodek et al. BMC Systems Biology 2013 7:15   doi:10.1186/1752-0509-7-15

Open Data