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KGML (KEGG Markup Language)

XML representation of KEGG pathway maps
The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and modeling of gene/protein networks and chemical networks. The KGML files for metabolic pathway maps contain two types of graph object patterns, how boxes (enzymes) are linked by "relations" and how circles (chemical compounds) are linked by "reactions". The KGML files for non-metabolic pathway maps contain only the aspect of how boxes (proteins) are linked by "relations". The prefix for the pathway map identifiers indicates the following:
  • ko - reference pathway map linked to KO entries (K numbers)
  • rn - reference pathway map linked to REACTION entries (R numbers)
  • ec - reference pathway map linked to ENZYME entries (EC numbers)
  • org (three- or four-letter organism code) - organism-specific pathway map linked to GENES entries (gene IDs)
(Note) The "map" prefix represents the internal format of KGML+ (KGML+SVG), which is used for generating ko/rn/ec files for metabolic pathways and ko files for non-metabolic pathways.


Access method

The KGML file may be obtained from the "Download KGML" link for each pathway map or by the get method of KEGG API.

Last updated: August 29, 2016
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