Taxonomy mapping is the process to map genomic contents of KOs (K numbers), modules (M numbers) and other objects to a taxonomy file in the form of Brite hierarchy. The result is usually viewed with the KEGG taxonomy browser, which is implemented as a special-purpose Brite hierarchy viewer.
Three-level taxonomic groups
The following interface returns a summary view of taxonomy mapping showing the number of KEGG organisms and viruses that contain given KOs and/or modules in the three levels of taxonomic groups (see details in: KEGG organism and virus groups).
The following interface gives a summary of taxonomic grouping for a given list of user-defined KEGG organism codes. The list may be preceded by '#name' to name the list. Multiple lists may be entered by using multiple # lines.
Taxonomy files
The KEGG database uses the NCBI taxonomy for classification of cellular organisms and viruses. For cellular organisms, the three- or four-letter KEGG organism codes are classified somewhat differently in the following Brite hierarchy files.
08601 is a manually created taxonomy file using the simple hierarchy defined in the KEGG organism groups and the predefined order of organism codes with hsa (Homo sapiens) at the top.
08610 is computationally generated using the abbreviated lineage of the NCBI taxonomy keeping the order of organism codes defined in 08601. In addition, 08610 contains taxonomy IDs for GENES Addendum (ag) entries. 08611 is another computationally generated file for the KEGG organisms with fixed levels of taxonomic ranks: phylum, class, order, family, genus and species.
For viruses, the taxonomy IDs of KEGG Viruses (GENOME vtax category and GENES vg category) are classified according to the NCBI taxonomy, which is based on the ICTV taxonomy, with the Baltimore classification added by KEGG.
Both of these Brite hierarchy files are computationally generated and the lowest-level taxonomy IDs are linked to GENOME vtax entries. In the 08620 file the taxonomy IDs are shown in the full lineage of NCBI virus taxonomy, while the 08621 file is organized in the fixed levels of taxonomic ranks: realm, kingdom, phylum, class, order, family, genus and species.
Taxonomy browser
The fixed-level taxonomy files of 08611 for cellular organisms and 08621 for viruses are used as default for taxonomy mapping. The browser has a zooming capability to adjust the bottom level of the taxonomic tree, for example, family or class in eukaryotes and species or genus in prokaryotes.
The taxonomic distribution of a single KO or module can be viewed from its entry page (such as K22014) through or button. Taxonomy mapping is performed using the default taxonomy file of 08611 or 08621.
Taxonomy mapping of cellular organisms
This interface displays taxonomic distributions of KOs (K numbers) and modules (M numbers) as genomic features, optionally combined with user-defined data such as for phenotypic features using the Join operation of KEGG Mapper.
Taxonomy mapping of viruses
This interface uses VOGs (virus ortholog groups) in addition to KOs for the virus taxonomy file.
