KEGG BRITE Functional Hierarchies

BRITE hierarchy files

The KEGG BRITE database is a collection of BRITE hierarchy files, called htext (hierarchical text) files, with additional files for binary relations. The htext file is manually created with in-house software called KegHierEditor. The htext file contains "A", "B", "C", etc. at the first column to indicate the hierarchy level, and may contain multiple tab-delimited columns. Thus, the htext file is like an Excel file with the additional first field for the hierarchy level. Here is an example.
A Metabolism
B   Carbohydrate Metabolism
C     00010 Glycolysis / Gluconeogenesis [PATH:ko00010]
D       K00844  HK; hexokinase [EC:]
D       K12407  GCK; glucokinase [EC:]
D       K00845  glk; glucokinase [EC:]
D       ......
The BRITE hierarchy file is created to represent functional hierarchy of KEGG objects identified by the KEGG Identifiers; for example, pathway-based gene classification or protein family classification by the K numbers, compound classification by C numbers, drug classification by D numbers, and disease classification by H numbers. The tab-delimited columns may be used to add attributes of KEGG objects or to indicate relationships between hierarchies.

The JOIN operation shown in the KEGG BRITE page can be used to add columns by combining a BRITE hierarchy file and a binary relation file. The file name extensions of these two file types are the following:
  • filename.keg - hierarchy (htext) file
  • filename.xl - binary relation file
KEGG objects can be searched and colored by the KEGG Mapper tools.

Convention of brite number prefix

Each BRITE hierarchy file is identified by the combination of 2-4 letter code and 5 digit number (see KEGG Identifiers). The prefix has the following meaning:
  • br - Reference hierarchy
  • jp - Reference hierarchy in Japanese
  • ko - Reference hierarchy (KO)
  • org - Organism-specific hierarchy
Thus, the "ko" hierarchy file is manually created for the functional classifications of genes and proteins using the K numbers. Organism-specific hierarchy files are then computationally generated by converting K numbers to gene identifiers in each organism. The "br" hierarchy file is created for the functional classifications of chemical compounds, reactions, drugs, diseases, organisms, etc. using the KEGG identifiers other than the K numbers.

Last updated: June 1, 2011