|
| |
KEGG Identifiers
KEGG Object Identifier
|
KEGG objects are biological entities from molecular to higher levels.
Each object (except for GENES) is identified by the KEGG object identifer, consisting of a five-digit number prefixed by an upper-case alphabet, such as K05032 and D00336, or prefixed by a 2-4 letter code for PATHWAY and BRITE, such as map00010 and br08301.
|
KEGG Organism Code
|
Each KEGG object can be uniquely identified without the database name becuase of the different prefix, but the general format to retrieve a database entry in KEGG and all other GenomeNet databases is:
db:entry
where "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).
The above examples can then be written as ko:K05032 and drug:D00336 (or dr:D00336).
In addition to the internally used T number shown above, an organism in KEGG is given a three-letter KEGG organism code (with prefix "d" for draft genome and "e" for EST contigs), 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 (see below).
The KEGG organism code is also used as a prefix to identify organism-specific pathway maps or BRITE functional hierarchies, such as hsa04930 and mmu04000.
| Prefix |
Content |
map
ko
ec
rn
br
"org" |
Reference pathway
Reference pathway (KO) or Reference BRITE hierarchy (KO)
Reference pathway (EC)
Reference pathway (Reaction)
Reference BRITE hierarchy (BR)
Organism-specific pathway or BRITE hierarchy
|
|
|
KEGG GENES Entry Name
|
Entry names of the KEGG GENES database are usually locus_tags given by the International Nucleotide Sequence Database Collaboration (INSDC).
The major sequence databases such as NCBI and UniProt/Swiss-Prot use different sets of gene/protein identifiers.
In order to facilitate the use of KEGG, automatic name conversion has been implemented for these identifiers.
|
KEGG Namespace
|
The KEGG identifiers, consisting of the KEGG object identifiers (prefix + five-digit numbers), the GENES entry names (locus_tags), and the enzyme identifiers (EC numbers), form the KEGG namespace.
The KEGG identifiers summarized below are highly linked within the KEGG namespace representing different types of biological relationships.
| Database |
Identifier |
Remark |
| PATHWAY |
map number |
Corresponds to a set of K/C/D/G/R numbers |
| BRITE |
ko/br number |
Corresponds to a set of K/C/D/G/R/T numbers |
| ORTHOLOGY |
K number |
Corresponds to a set of GENES entry names |
| GENES |
Entry name
(locus_tag) |
|
| LIGAND |
C/D/G/R number
RP number
EC number |
|
|
Links to Outside Databases
|
In addition to the links within the KEGG namespace, the KEGG identifiers are linked to outside database entries.
The links usually represent the same biological meaning, such as the same gene or protein in the same organism, enabling the user to integrate information from different sources.
In this respect, KEGG is a portal site to more specialized databases in various fields of biomedical sciences.
A full list of outside links can be obtained from LinkDB.
|
Last updated: July 1, 2010
|
|
