Databases and Systems

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3. to organize a database of all chemical compounds in the cell and link each
compound to a pathway component, and
4.
to develop computational technologies for pathway comparison, reconstruction,
and analysis.
KEGG is publicly made available as part of the Japanese GenomeNet Service [2].
The WWW addresses that are relevant to this chapter are summarized in Table 1.
Data Representation in KEGG
Level of abstraction
Table 1. The Japanese GenomeNet service
As illustrated in Figure 1, a cysteine is a network of carbon, nitrogen, oxygen,
hydrogen, and sulfur atoms at the atomic level, but it is abstracted to letter C at the
molecular level where a protein is represented by a one-dimensional network of
twenty letters (amino acids). In the next network level the protein is abstracted to a
symbol, Ras, and the wiring among different symbols (proteins) is the major concern
as in this case of Ras signal transduction pathway. Most of the current molecular
biology databases contain the data at either the molecular level or the atomic level
focusing on the information that is associated with protein and nucleic acid
molecules, such as the sequence databases and the 3D structural databases.
Consequently, the majority of the current computational methods in molecular
biology involves comparison and analysis of sequence data or 3D atomic coordinate
data. The main role of KEGG is to fill the gap at the network level by computerizing
current knowledge of biochemical pathways and by developing associated
computational technologies. KEGG also intends to fill another gap at the atomic
level, which is the lack of good public resources for chemical compounds.