KGML (KEGG Markup Language)
XML representation of KEGG pathway maps
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.
The KGML files for metabolic pathway maps contain two types of graph object patterns, how boxes (enzymes) are linked by "relations" and how circles (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 K numbers (KO identifiers)
- ec - reference pathway map linked to EC numbers
- org (three- or four-letter organism code) - organism-specific pathway map linked to genes
Documents
Other formats
In addition to the KGML format, the KEGG pathway maps are now available in the BioPAX level 2 format.
The conversion from KGML to BioPAX has been done by using the BN++ library [reference].
Access methods
The entire set of KGML files or BioPAX files may be downloaded from the FTP site (academic users only).
Non-academic users are requested to obtain a licensing agreement. Please refer to the page below.
Last updated: October 1, 2009
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