Table 1

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)” [16]. 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

Open Data