Integrated Database of Microbial Genomes and Cellular Functions

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The roles of biological databases are changing in two important aspects to meet the needs for understanding biological systems from genomic information. First, the data contents about molecular sequences, molecular structures, and molecular functions are certainly not sufficient. It is necessary to somehow capture higher-level structures and functions, such as molecular interaction networks and cellular processes, and create new databases that integrate both molecular and higher-level information. Second, although the current mechanism of data submissions by individual authors works well for the sequence and 3D structure databases, it is not appropriate for keeping up with the expanding biological knowledge in the research community. In this project we developed BSORF (bacillus.genome.jp) and CYORF (cyano.genome.jp) databases for the Bacillus subtilis and cyanobacteria research communities, respectively. For the first aspect we utilized our KEGG resource for pathway and network information, which is highly integrated with the BSORF and CYORF databases. In addition, BSORF contains a large set of microarray gene expression data and information about essential genes, both of which were obtained by the Japanese research community. For the second aspect, we have been promoting the mechanism of community annotation database where individual researchers in the community not only obtain information from the database, but also enter their knowledge into the database, so that the community as a whole can share most up-to-date information and knowledge. CYORF is the most successful community annotation database, which is now widely accepted by the international cyanobacteria research community. We also developed comparative genomics tools for automatic classification of orthologous genes and for detection of conserved gene clusters in multiple genomes. Both tools are made available in KEGG (www.genome.jp/kegg/).