|BioPAX instances and SBO terms corresponding to KGML entry types|
|Entry type||BioPAX element||SBO term|
|compound||smallMolecule||247 (simple chemical)|
|enzyme||protein||252 (polypeptide chain)|
|gene||protein||252 (polypeptide chain)|
|ortholog||protein||252 (polypeptide chain)|
|group||complex||253 (non-covalent complex)|
|map||pathway||552 (reference annotation)|
This table depicts the conversion of KGML entries to BioPAX or SBML. The conversion depends on the KGML entry type attribute. For BioPAX, different class instances are initialized. Conversions to SBML always involve the creation of a species with the given SBO term for each KGML entry. The KGML specification states that an entry of type ‘gene’ “is a gene product (mostly a protein)”. Additionally, a ‘group’ “is a complex of gene products (mostly a protein complex)” . For compatibility with previous KGML versions, the deprecated type ‘genes’ corresponds to ‘group’ since KGML v0.6.1. Further, entries of type ‘reaction’ are not listed in the table, but discussed in a separate section.
Wrzodek et al.
Wrzodek et al. BMC Systems Biology 2013 7:15 doi:10.1186/1752-0509-7-15