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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 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
rclass
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
dgroup
Drug
Drug group
D
DG
D01441
DG00710
<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
<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).

KEGG DB Links

KEGG objects are highly integrated by mutual links within KEGG, and are also linked to related entries in outside databases. The following table shows the links maintained by KEGG. There are additional links maintained by GenomeNet (see LinkDB), including those created by outside databases.

Database Internal links Outside links
ID conversion1 Other
pathway module ko <org> genome compound glycan reaction rclass enzyme network disease drug pubmed go umbbd
brite ko <org> genome compound glycan reaction disease drug go
module pathway ko <org> genome compound glycan reaction enzyme disease pubmed
ko pathway brite module genes <org> vg vp ag reaction rclass enzyme network disease drug pubmed cog go tc cazy
<org> pathway brite module ko genome enzyme (network disease drug)2 ncbi-geneid ncbi-proteinid uniprot pfam <original_dbs>3
vg ko genome enzyme ncbi-geneid ncbi-proteinid uniprot pfam taxonomy refseq
vp ko enzyme ncbi-proteinid genbank
ag ko genome enzyme pubmed ncbi-proteinid uniprot pfam taxonomy genbank
genome pathway brite module <org> vg ag compound disease pubmed taxonomy assembly genbank refseq
compound pathway brite module genome glycan reaction enzyme network disease drug pubchem chebi cas lipidmaps lipidbank knapsack pdb-ccd 3dmet nikkaji
glycan pathway brite module compound reaction enzyme pubchem chebi ccsd glytoucan jcggdb lipidbank glycoepitope
reaction pathway brite module ko compound glycan rclass enzyme rhea
rclass pathway ko reaction enzyme
enzyme pathway module ko <org> vg vp ag compound glycan reaction rclass explorenz iubmb expasy umbbd brenda cas
network pathway ko hsa compound variant disease pubmed
variant
(hsa_var)
network drug pubmed clinvar dbsnp dbvar cosmic omim
disease pathway brite module ko hsa genome compound network drug pubmed icd-11 icd-10 mesh omim medlineplus
drug pathway brite ko hsa compound variant disease dgroup atc jtc ndc yj pubchem chebi cas pdb-ccd ligandbox nikkaji
dgroup drug

1 Outside links for ID conversion allow, for example, outside identifiers to be used in KEGG Mapper analysis. The Conv ID tool in KEGG Mapper may be used to convert GeneIDs, ProteinIDs or UniProt IDs to KEGG identifiers.
2 Parentheses for hsa (Homo sapiens) only.
3 <original_dbs> include: mirbase ensembl cyorf cyanobase nite rhizobase genedb pasteur flybase vega vectorbase ... (total of >70 dbs)


Last updated: January 1, 2024

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