KEGG Objects

KEGG objects are biological entities from molecular to higher levels that are represented as database entries in KEGG, such as genes and protein, small molecules, reactions, pathways, diseases and drugs.

KEGG Identifier

The KEGG object identifer or simply the KEGG identifier (kid) is a unique identifier for each KEGG object, which is also the database entry identifier. Generally it takes the form of a prefix followed a five-digit number as shown below:

Database Object Prefix Example
pathway KEGG pathway map map, ko
ec, rn
<org>
 
map00010
hsa04930
brite BRITE functional hierarchy br, jp
ko

<org>
br08303
ko01003
module KEGG module M <org>_M M00010
ko KO functional ortholog K K04527
genome KEGG organism
(complete genome)
T T01001 (hsa)
genes <org>
vg
ag
Gene / protein hsa:3643
vg:155971
ag:CAA76703
compound Small molecule C C00031
glycan Glycan G G00109
reaction
rclass
Reaction
Reaction class
R
RC
R00259
RC00046
enzyme Enzyme ec:2.7.10.1
disease Human disease H H00004
drug
dgroup
Drug
Drug group
D
DG
D01441
DG00710
environ Health-related substance E E00048
<org> represents three- or four-letter organism code

Exceptions are GENES identifiers and EC numbers for enzymes, which follow the general form of the the DBGET retrieval system (see About DBGET). Each entry in DBGET is identified by
<database>:<entry>
where <database> is the database name and <entry> is the entry name or the accession number (see DBGET for the list of database names and abbreviations).

The KEGG identifiers with database-dependent prefixes are often called D numbers, K numbers, C numbers, etc. Since these numbers are unique across the KEGG databases, <database> may be omitted in the DBGET system. For example,
D01441
dr:D01441
drug:D01441
are all equivalent.

KEGG Organism Code

In addition to the T number shown above, an organism in KEGG is given a three- or four-letter KEGG organism code, which is treated like a database name. Therefore, individual genes in an organism can be identified in the following way:
<org>:<gene>
where <org> is the KEGG organism code and <gene> is the KEGG GENES entry name. The KEGG organism code is also used as a prefix to identify organism-specific pathway maps or BRITE functional hierarchies (see: Pathway maps and Brite hierarchies).


Last updated: June 23, 2017