KGML (KEGG Markup Language) for Exchanging the KEGG Graph Objects

Shuichi Kawashima, Susumu Goto, Toshiaki Katayama, Mika Hirakawa,
Minoru Kanehisa

The KEGG pathway maps are graphical image maps representing networks
of interacting molecules responsible for specific cellular
functions. There are two types of KEGG pathways:

 * reference pathways which are manually drawn and
 * organism-specific pathways which are computationally generated
   based on reference pathways.

The KEGG Markup Language (KGML) is an exchange format of the KEGG
graph objects, especially the KEGG pathway maps that are manually
drawn and updated. KGML enables automatic drawing of KEGG pathways and
provides facilities for computational analysis and modeling of protein
networks and chemical networks. 

In KGML the pathway element specifies one graph object with the entry
elements as its nodes and the relation and reaction elements as its
edges. The relation and reaction elements indicate the connection
patterns of rectangles (gene products) and the connection patterns of
circles (chemical compounds), respectively, in the KEGG pathways. The
two types of graph objects, those consisting of entry and relation
elements and those consisting of entry and reaction elements, are
called the protein network and the chemical network, respectively.
Since the metabolic pathway can be viewed both as a network of
proteins (enzymes) and as a network of chemical compounds, another
distinction of KEGG pathways is:

 * metabolic pathways viewed as both protein networks and chemical
   networks and
 * regulatory pathways viewed as protein networks only.

Each KGML file may be acquired from the KGML top page:
  URL:http://www.genome.ad.jp/kegg/xml/