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:
<org> represents three- or four-letter organism code
Exceptions are GENES identifiers (including variant 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
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,
Database | Object | Prefix | WebLinks example | |||
pathway | KEGG pathway map | map | <org> ko, ec, rn |
map00010 hsa04930 |
map00010 hsa04930 |
|
brite | BRITE functional hierarchy | br, jp ko |
<org> |
br:08303 br:01002 |
br08303 ko01002 |
|
module | KEGG module | M | <org>_M | M00010 | M00010 | |
ko | Functional ortholog | K | K04527 | |||
genes | <org> vg vp ag |
Gene / protein | hsa:3643 vg:155971 vp:155971-1 ag:CAA76703 |
|||
genome | KEGG organism (complete genome) |
T | T01001 (hsa) |
T01001 | ||
compound | Small molecule | C | C00031 | |||
glycan | Glycan | G | G00109 | |||
reaction | Reaction Reaction class |
R RC |
R00259 RC00046 |
|||
enzyme | Enzyme | ec:2.7.10.1 | ||||
network | Network element Network variation map |
N nt |
N00002 nt06210 |
nt06210 |
||
variant | Human gene variant | hsa_var:25v1 | ||||
disease | Human disease | H | H00004 | |||
drug | Drug Drug group |
D DG |
D01441 DG00710 |
Exceptions are GENES identifiers (including variant 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,
D01441are all equivalent.
dr:D01441
drug:D01441
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: November 1, 2022