Databases and Systems

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Data Organization in KEGG
Biochemical pathways
KEGG contains most of the known metabolic pathways, especially for the
intermediary metabolism, that are represented by about 100 graphical diagrams
(pathway maps). In addition, we are adding various types of regulatory pathways
such as membrane transport, signal transduction, cell cycle, transcription, and
translation, as well as the information of molecular assemblies. Each pathway
diagram is drawn and continuously updated manually. For metabolic pathways the
manually drawn diagrams are considered as references of biochemical knowledge
containing all chemically identified reaction pathways. The organism-specific
pathways are then automatically generated by matching the enzyme genes in the gene
catalog with the enzymes on the reference pathway diagrams according to the EC
number. The matched enzymes are colored green in the pathway diagrams. This
matching process is possible because the intermediary metabolism is relatively well
conserved among different organisms. In contrast, the regulatory pathways are too
divergent to be represented in a single reference diagram; they are drawn separately
for each organism.
Gene catalogs and genome maps
The information of genes and genomes is taken from GenBank and organized as the
gene catalog and the genome map. The gene catalog contains classifications of all
known genes for each organism. Depending on how one views the function, genes
may be classified in different ways. KEGG provides its own classification scheme
according to the pathway classification, as well as another scheme by the original
authors which is often a variant of Riley's classification [6]. As mentioned the
functional assignment of genes is re-examined by KEGG. The genome map is
presented to help understand the positional information of genes, such as an operon
structure, and its relationship with the pathways and assemblies. Genome maps are
manipulated graphically by Java applets.
In order to cope with an increasing number of complete genomes, we are trying to
automate as much as possible the EC number assignment that is critical to generate
organism-specific metabolic pathways and the gene function assignment. Both
assignments are based not only on sequence similarity, but also on additional
information including the positional information in the genome and the orthologous
relation with different species. Since the operon structure is widespread in bacteria
and archaea, the genome map browser has turned out to be an indispensable tool for
gene function assignment.
Ortholog group tables
Sequence similarity search against the existing sequence databases often generates a
long list of hits, which requires human efforts to screen out orthologous relations that