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 Object Identifier
The identifier of each database entry is generally in the form of
(org) represents three-, four-, or five-letter organism code
The thirteen databases are all manually created by KEGG. The remaining two databases, KEGG GENES derived from RefSeq and KEGG ENZYME derived from ExplorEnz, are also given KEGG-original annotations.
db:entrywhere "db" is the database name and "entry" is the entry name or the accession number (see DBGET for the list of database names and abbreviations). However, "db" may be omitted in thirteen of the fifteen databases shown below, because the entry name, called the KEGG object identifier consisting of a database-dependent prefix and a five-digit number, is unique across the databases. The KEGG object identifiers are often called D numbers, K numbers, C numbers, etc. The D number example shown below D01441 is thus equivalent to dr:D01441 or drug:D01441.
| Database | Object | Prefix | Example |
| KEGG PATHWAY | Pathway map | map, ko, ec, rn, (org) | hsa04930 |
| KEGG BRITE | Functional hierarchy | br, jp, ko, (org) | ko01003 |
| KEGG MODULE | KEGG module | M, (org)_M | M00010 |
| KEGG DISEASE | Human disease | H | H00004 |
| KEGG DRUG | Drug | D | D01441 |
| KEGG ENVIRON | Crude drug, etc. | E | E00048 |
| KEGG ORTHOLOGY | KO group | K | K04527 |
| KEGG GENOME | KEGG organism | T | T01001 (hsa) |
| KEGG GENES | Gene / protein | hsa:3643 | |
| KEGG COMPOUND | Small molecule | C | C00031 |
| KEGG GLYCAN | Glycan | G | G00109 |
| KEGG REACTION | Reaction | R | R00259 |
| KEGG RPAIR | Reactant pair | RP | RP04458 |
| KEGG RCLASS | Reaction class | RC | RC00046 |
| KEGG ENZYME | Enzyme | ec:2.7.10.1 |
The thirteen databases are all manually created by KEGG. The remaining two databases, KEGG GENES derived from RefSeq and KEGG ENZYME derived from ExplorEnz, are also given KEGG-original annotations.
KEGG Organism Code
In addition to the T number shown above, an organism in KEGG is given a three-letter KEGG organism code (with prefix "d" for automatically annotated genomes), which is treated like a database name. Therefore, individual genes in an organism can be identified in the following way:
org:genewhere "org" is the KEGG organism code and "gene" is the KEGG GENES or DGENES entry name (see below). 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).
Links to Outside Databases
The KEGG objects are linked to numerous outside database entries with the same biological meaning, such as the same gene or protein in the same organism, enabling the user to integrate information from different sources (see the list of outside links in the GenomeNet LinkDB page).
The KEGG GENES entry names, which are usually NCBI GeneIDs or locus_tags, can be converted to/from the identifiers of the major sequence databases through the GenomeNet LinkDB system. The following interface allows conversion from NCBI or UniProt.
The KEGG GENES entry names, which are usually NCBI GeneIDs or locus_tags, can be converted to/from the identifiers of the major sequence databases through the GenomeNet LinkDB system. The following interface allows conversion from NCBI or UniProt.
Last updated: January 4, 2012