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 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 |
|||
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.
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.
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)
| 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