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README for the "brite" subdirectory
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KEGG BRITE is a collection of BRITE hierarchy files, called htext
(hierarchical text) files, together with a smaller collection of BRITE
binary relation files. They represent hierachical classifications of
and relationships among KEGG objects, such as genes, metabolites,
drugs, and diseases. The htext file contains "A", "B", "C", etc. at
the first column to indicate the hierarchy level, such as: 

    A Metabolism
    B   Carbohydrate Metabolism
    C     00010 Glycolysis / Gluconeogenesis [PATH:ko00010]
    D       K00844  HK; hexokinase [EC:2.7.1.1]
    D       K12407  GCK; glucokinase [EC:2.7.1.2]
    D       K00845  glk; glucokinase [EC:2.7.1.2]
    D       ......

and may contain tab-delimited columns for the attributes of KEGG objects.

Each BRITE hierarchy file (with extension .keg) is identified by the
combination of the two- or three-letter prefix and the five-digit
number, such as ko00001. The prefix has the following meaning:

    br - Reference hierarchy
    jp - Reference hierarchy in Japanese
    ko - Reference hierarchy (KO)
    org - Organism-specific hierarchy

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

The "ko" hierarchy files are manually created for the functional
classifications of genes and proteins using the K numbers (KEGG
ORTHOLOGY identifiers). Organism-specific hierarchy files are then
computationally generated by converting K numbers to gene identifiers
in each organism. The "br" hierarchy files are manually created for the
functional classifications of chemical compounds, reactions, drugs,
diseases, organisms, etc. using the KEGG object identifiers other than
the K numbers. 

The following tarballs are created in this directory for the BRITE
hierarchy files grouped by the prefix code:

    br.tar.gz
    jp.tar.gz
    ko.tar.gz
    organisms/org.tar.gz

In addition, the following tarball contains the BRITE binary relation
files (with extension .xl):

    xl.tar.gz

The list of currently available BRITE hierarchy files is shown in:

    brite.list
    brite_jp.list (Japanese files)

Note that the hierarchy file name containing "_" means that the file is
computationally generated by combining a hierarchy file and a binary
relation file. For example,

    br08303_target.keg = br08303.keg + drug2target.xl

represents a drug classification file with target information in an
additional column.

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Updated: May 16, 2011

(c) Kanehisa Laboratories