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Integrated Database of Microbial Genomes and Cellular Functions

微生物基因组和细胞功能综合数据库

基本信息

批准号：
15013227
负责人：
KANEHISA Minoru
金额：
$ 15.36万
依托单位：
Kyoto University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research on Priority Areas
财政年份：
2003
资助国家：
日本
起止时间：
2003 至 2004
项目状态：
已结题

项目摘要

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/).

为了满足从基因组信息中理解生物系统的需要，生物数据库的作用在两个重要方面发生了变化。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捉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。其次，虽然目前个人作者提交数据的机制对于序列和3D结构数据库来说很好，但它不适合跟上研究界不断扩大的生物学知识。在本项目中，我们分别开发了枯草芽孢杆菌和蓝藻研究界的BSORF （Bacillus .genome.jp）和CYORF （cyano.genome.jp）数据库。在第一个方面，我们利用KEGG资源获取路径和网络信息，该资源与BSORF和CYORF数据库高度集成。此外，BSORF还包含大量由日本研究界获得的微阵列基因表达数据和必需基因信息。第二方面，我们一直在推进社区标注数据库机制，使社区内的个人研究人员不仅可以从数据库中获取信息，还可以将自己的知识输入到数据库中，使整个社区能够共享最新的信息和知识。CYORF是目前最成功的社区注释数据库，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，用于自动分类同源基因和检测多个基因组中的保守基因簇。这两个工具都可以在KEGG （www.genome.jp/kegg/）中获得。