Databases and Systems

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Different types of networks
Figure 2: Data representation in KEGG.
Figure 2 illustrates the data hierarchy in KEGG that consists of elements, binary
relations, and networks, and also examples of different types of networks. A network
is any type of relationship among a set of elements. For example, the biochemical
pathway is a network of interacting molecules and the genome is a one-dimensional
network of genes. The information of neighbors that can be computed by sequence
similarity search or 3D structural similarity search among a set of molecules also
forms a complex network. The similarity relationship is often better organized in the
form of a hierarchy, such as the superfamily classification or the 3D fold
classification, which is still another type of network.
Table 2 summarizes the actual implementation of different types of networks in
KEGG. The biochemical pathway is represented by the graphical pathway map,
which is handled as a GIF image map by HTML, CGI scripts, and Java applets. The
genomic information is represented by the gene catalog that is a functional hierarchy
of genes and the graphical genome map. The gene catalog as well as the catalog of
proteins and other molecules is handled by the CGI script for, what we call,