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README for the "xml/kgml" subdirectory
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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)
    ec  - reference pathway map linked to ENZYME entries (EC numbers)
    rn  - reference pathway map linked to REACTION entries (R numbers)
    org - organism-specific pathway map linked to GENES entries (gene ids)

where "org" is a three-letter organism code.

The following tarballs are created in the "metabolic" and "non-metabolic"
subdirectories for the KEGG pathway maps grouped by the prefix code:

    metabolic
      ko.tar.gz
      ec.tar.gz
      rn.tar.gz
      organisms/org.tar.gz
    non-metabolic
      ko.tar.gz
      organisms/org.tar.gz


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Updated: March 6, 2012

(c) Kanehisa Laboratories