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README for the "pathway" subdirectory
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KEGG PATHWAY is a collection of manually drawn KEGG pathway maps
representing our knowledge on the molecular interaction and reaction
networks for metabolism and various other cellular processes, organismal
systems, and human diseases. The molecular networks are represented
in terms of the KEGG Orthology (KO) groups (drawn as boxes), so that
experimental evidence in specific organisms can be generalized to other
organisms through genomic information.

Each pathway map is identified by the combination of the two- or three-
letter prefix and the five-digit number, such as map00010. The prefix
has the following meaning:

    map - Reference pathway map
    ko  - Reference pathway (KO) map
    ec  - Reference pathway (EC) map
    rn  - Reference pathway (reaction) map
    org - Organism-specific pathway map

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

Only the "map" reference pathway maps are manually drawn; all the other
maps are computationall generated with coloring of boxes in: blue for
"ko", "ec", and "rn" maps and green for "org" maps. For metabolic
pathways, each box in the "map" maps is linked to the K number (KO
identifeir), the EC number, and the R number (reaction identifier).
The KO, EC, and reaction maps are linked to only one of them. For all
metabolic and non-metabolic pathway maps, K numbers are converted to
gene identifiers in each organism to generate organism-specific
pathways. 

The following tarballs are created in this directory for the KEGG
pathway maps grouped by the prefix code:

    map.tar.gz
    ko.tar.gz
    ec.tar.gz
    rn.tar.gz
    organisms/org.tar.gz

The tarball contains all available pathway maps, each consisting of
of two file with the extension:

    .png  - pathway image file
    .conf - contains coordinates of map objects in the image file

and auxiliary tab-delimited files showing which pathways the map
objects appear.

In addition, this directory contains higher-resolution image files

    map2x.tar.gz

and the following files:

    pathway.gz     DBGET flat file for all PATHWAY entries
    pathway.list   List of currently available pathway maps
    map_title.tab  Same as above (without classification hierarchy)
    links.tar.gz   ID mapping files of PATHWAY to/from other KEGG DBs
                   and PubMed


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Updated: October 24, 2024

(c) Kanehisa Laboratories