Construction and Retrieval of Highly Integrated Biological Databases

高度集成的生物数据库的构建和检索

基本信息

批准号：
12208007
负责人：
GOTO Susumu
金额：
$ 58.82万
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：
2000
资助国家：
日本
起止时间：
2000 至 2004
项目状态：
已结题

项目摘要

We have constructed a database of molecular interactions and developed methods for extracting novel biological knowledge from it. It is important for such a database to be able to handle chemical information as well as genomic and proteomic information as an integrated manner. Considering this viewpoint, we have achieved the following three main results.1.BRITE databaseWe have developed the BRITE database storing direct and indirect molecular interaction data as binary relations. It mainly consists of protein interaction data from yeast two-hybrid systems, neighboring enzyme relations in the KEGG metabolic pathway, and relationship between transcription factors and their target genes in the KEGG regulatory pathway. BRITE has a facility to retrieve these binary data and display them as a network.2.Ontology extraction from genome databasesWe implemented a general framework for extracting relationships among data. Using the association rule discovery method that is one of the well-known d … More ata mining methods, it quickly discovers common and specific features to a given set of entries. Next we defined relationship among keywords and entries by constructing a huge dictionary derived from genome databases. We also constructed a GRID environment for developing huge databases.3.Integration of chemical information into the database and analysis of network topologiesWe developed a representation format for secondary structures of chemical compounds in terms of reactivity and a method for comparing chemical structures based on the format. We also developed an algorithm to infer rules of chemical structure conversion in the enzyme reactions, and construct a database of reactant pairs by applying it. This database was further applied to a prediction of novel enzyme reaction pathways. Regarding the topology analysis, two networks created by the pairs of chemical compounds and enzyme relations were our targets. We obtained new insights into the relationship between the two networks and functional modules in the metabolic network. Less

我们已经构建了一个分子相互作用的数据库，并开发了从中提取新生物学知识的方法。对于这样的数据库而言，能够作为综合方式处理化学信息以及基因组和蛋白质组学信息很重要。考虑到这一观点，我们已经达到了以下三个主要结果。1.Brite数据库We开发了Brite数据库，该数据库存储直接和间接分子相互作用数据作为二进制关系。它主要由来自酵母两杂交系统的蛋白质相互作用数据，KEGG代谢途径中的相邻酶关系以及转录因子及其靶基因之间的关系中的KEGG调节途径之间的关系。 Brite具有检索这些二进制数据并将其显示为网络的功能。使用关联规则发现方法是众所周知的D…更多ATA采矿方法，它很快发现了一组条目的常见和特定特征。接下来，我们通过构建源自基因组数据库的巨大词典来定义关键字和条目之间的关系。我们还构建了一个用于开发巨大数据库的网格环境。3。化学信息到数据库中的融合和网络拓扑分析我们开发了一种用反应性的化合物二级结构的表示形式，以及一种基于格式的化学结构的方法。我们还开发了一种算法来推断酶反应中化学结构转化的规则，并通过应用它来构建反应物对的数据库。该数据库进一步应用于新型酶反应途径的预测。关于拓扑分析，我们的目标是由化合物和酶关系对创建的两个网络。我们获得了对代谢网络中两个网络和功能模块之间关系的新见解。较少的