Summary of Research Project Results under JSPS FY2004
"Research for the Future Program"

1. Research Institution   Kyoto University
2. Research Area Life Sciences
3. Research Field Genome Research
4. Term of Project FY 2000 - FY 2004
5. Project Number 00L01409
6. Title of Project Biological Systems Database and Genome Information Science

7. Project Leader

Name Institution, Department Title of Position
Minoru, Kanehisa Kyoto University, Institute for Chemical Research Professor

8. Core Member

Name Institution, Department Title of Position
Susumu, Goto Kyoto University, Institute for Chemical Research Associate Professor

9. Summary of Research Results

KEGG ( is a bioinformatics resource for understanding higher-level functional meanings and utilities of the cell or the organism from its genome information. It integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database) with the repertoire of genes and proteins in individual organisms (GENES database), and also with the information about biochemical compounds and reactions (LIGAND database). During the five years of this project we have significantly expanded the PATHWAY database, adding not only metabolic pathways but also various regulatory pathways. In addition, an XML version of pathway maps was made available to facilitate computational analysis of KEGG pathways. For the GENES database we introduced the KO (KEGG Orthology) grouping, and developed an automatic method of KO assignment and KEGG pathway mapping, enabling rapid analysis of genomic sequences and cDNA sequences for understanding higher-order functions. For the LIGAND database we developed graph-based algorithms for chemical structure comparison and glycan structure comparison, as well as a method to automatically detect and categorize chemical transformation patterns in enzymatic reactions based on the RC (Reaction Classification) system. This has enabled automatic assignment of EC numbers. The entire KEGG resource is made available at the KEGG website, as well as through the newly developed KEGG API for customization in users' own programs. With the KEGG resource we have undertaken new research on integrated analysis of genomic and chemical information. By organizing our knowledge on the universe of enzyme-catalyzed biochemical reactions and biosynthetic/biodegradation pathways, the universality and diversity of these reactions and pathways can now be linked to orthologs and paralogs in various genomes, and also to the core structures and terminal variations of various biochemical compounds.

10. Key Words

( 1 ) Genome ( 2 ) Proteome ( 3 ) Bioinformatics
( 4 ) Pathway ( 5 ) Network ( 6 ) Database
( 7 ) Ontology ( 8 ) Function prediction ( 9 ) Chemical genomics