KEGG GENOME is a collection of KEGG organisms, which are the organisms with complete genome sequences and each of which is identified by the three- or four-letter organism code. The genome entry (such as hsa) serves as an organism-specific entry point for viewing pathway maps, Brite hierarchies and KEGG modules, as well as for launching Genome Browser. The GENOME database also contains a collection of KEGG Viruses generated from RefSeq data and each identified by the virus taxonomy (vtax) identifier (see KEGG Virus for more details).


Most genomes are associated with genome maps showing chromosomal locations of genes, which can be viewed by a graphical interface of KEGG Genome Browse, a part of KEGG Web Apps.

KEGG organisms are manually organized in a simple hierarchy of taxonomic groups with predefined ordering of organisms starting with hsa (Homo sapiens). The hierarchy is shown in the following two Brite files with identical contents.

• 08601 KEGG organisms (Brite hierarchy file)
• 08606 KEGG organisms (Brite table file)

KEGG organisms are also shown in the following Brite hierarchy files, which are computationally generated from the NCBI taxonomy.

• 08610 KEGG organisms in the NCBI taxonomy
• 08611 KEGG organisms in taxonomic ranks

The ordering of KEGG organisms defined in 08601 is retained in 08610 and 08611. The file 08611 is created with the fixed levels of taxonomic ranks and used as default for taxonomy mapping and other purposes.

From the classification of KEGG organisms, the organism group names are defined:

• 08609 Organism group names defined in KEGG

They also correspond to taxonomic groups in the NCBI taxonomy as shown below.

• 08608 KEGG organism and virus groups

Excluding the distinction of eukaryotes and prokaryotes, the three-level organism groups are frequently used in KEGG. For example, the KEGG Syntax analysis reveals the similarity relationship of the six top level groups of animals, plants, fungi, protists, bacteria and archaea as shown here.

KEGG mapping for linking genomes to pathways is performed through the KO (KEGG Orthology) system. Given a set of KOs presented in the genome of an organism, matching pathway maps and complete modules can be generated, enabling interpretation of cellular and organism-level functions. The procedure has been generalized and is now applicable to an organism, an organism group, a metagenome and any combination of them.

The interface at the top of this page is an exension of the organism specific entry point, which now accepts the following:

1. KEGG Organism specified by organism code or T number
2. Organism group specified by predefined name
3. Organism group specified by NCBI taxonomy ID for a taxonomic rank
4. Metagenome specified by GenomeNet metagenome T number

Examples:

(Organism menu)
hsa	Homo sapiens (human) entry point to Organism info, Pathway map, Module, Brite hierarchy and Genome browser
(Genome comparison)
hsa eco	Homo sapiens (human) and Escherichia coli K-12 strain such as for comparison of Terpenoid backbone biosynthesis
(Organism group comparison)
plants animals	Plants vs. Animals such as for module-based comparison of Global metabolic pathways
(Host-microbiome relationship)
hsa T30003	Homo sapiens (human) + Human gut microbiome sample T30003 such as for KO-based combination of Global metabolic pathways
(Host-symbiont relationship)
api buc	Acyrthosiphon pisum (pea aphid) + Buchnera aphidicola such as for finding additional modules by combined KOs
27482 32199	Aphididae (family) + Buchnera (genus) such as for finding additional modules by combined KOs
(Host-vector-pathogen relationship)
hsa aga pfa	Homo sapiens (human) + Anopheles gambiae (mosquito) + Plasmodium falciparum