Integrated Database of Microbial Genomes and Cellular Functions

生物数据库的作用正在两个重要方面发生变化，以满足从基因组信息理解生物系统的需要。首先，关于分子序列、分子结构和分子功能的数据内容肯定是不够的。有必要以某种方式捕获更高层次的结构和功能，如分子相互作用网络和细胞过程，并创建整合分子和更高层次信息的新数据库。第二，虽然目前的数据提交机制，由个人作者的序列和三维结构数据库工作良好，它是不适合跟上不断扩大的生物学知识的研究社区。在这个项目中，我们开发了BSORF（bacillus.genome.jp）和CYORF（cyano.genome.jp）数据库的枯草芽孢杆菌和蓝藻研究社区，分别。对于第一个方面，我们利用我们的KEGG资源的途径和网络信息，这是高度集成的BSORF和CYORF数据库。此外，BSORF包含大量的微阵列基因表达数据和必需基因的信息，这两个数据都是由日本研究界获得的。在第二方面，我们一直推动社区注释数据库机制，让社区内的个别研究人员不单从数据库取得数据，更可将他们的知识输入数据库，令整个社区可以分享最新的信息和知识。CYORF是目前国际上最成功的蓝藻群落注释数据库，已被国际蓝藻研究界广泛接受。我们还开发了比较基因组学工具，用于自动分类直向同源基因和检测多个基因组中的保守基因簇。这两种工具都可在KEGG（www.genome.jp/kegg/）上查阅。

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/).