Construction of Federated Genome Knowledgebases by Grid Computing

通过网格计算构建联合基因组知识库

• 批准号: 15607013
• 负责人: MATSUDA Hideo
• 金额: $ 2.24万
• 依托单位: Osaka University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 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
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15607013/
• 关键词: Grid Computing; Genome Database; Database Federation; Knowledgebase; Genome Information Analysis; XML; データ検索インターフェース; バイオインフォマティクス

The genome-related data have been separately stored in different databases of which schemes and formats are different ; such as DDBJ/EMBL/GenBank for DNA nucleotide sequences, PIR and SWISS-PROT for protein sequences, and PDB for protein tertiary structures. Moreover, a number of databases have been constructed according to the domain of data or the purpose of databases. Recently, the number of genome-related databases reaches more than 700 databases. It is difficult for users to find new and valuable knowledge until new database management methods and new access methods are developed.From these viewpoints, this research aims at the following themes :(1)Ontology-based unified data access in different scientific domains.There are many types of data which belong to different domains ; namely, DNA nucleotides, proteins, and cellular components. For this reason, it is difficult to unify such databases into single common scheme. Thus we have developed ontologies and their usability technology as common descriptions of each data domain or interdisciplinary areas.(2)It is possible to make combinatorial explosion for the query processing of the federated databases. To cope with this issue, we have developed a technology for customizing a grid environment.

基因组相关数据分别存储在不同的数据库中，不同的数据库方案和格式不同；例如DNA核苷酸序列的DDBJ/EMBL/GenBank，蛋白质序列的PIR和SWISS-PROT，蛋白质三级结构的PDB。此外，根据数据的领域或数据库的用途，已经建立了许多数据库。目前，基因组相关数据库的数量已达700多个。只有开发出新的数据库管理方法和新的访问方法，用户才能发现新的有价值的知识。基于这些观点，本研究主要围绕以下主题展开：(1)基于本体的不同科学领域的统一数据访问。有许多类型的数据属于不同的领域；即DNA核苷酸、蛋白质和细胞成分。因此，很难将这些数据库统一为单一的通用方案。因此，我们开发了本体及其可用性技术，作为每个数据域或跨学科领域的通用描述。(2)对联邦数据库的查询处理进行组合爆炸是可能的。为了解决这个问题，我们开发了一种定制网格环境的技术。

项目成果

A Method for Clustering Expression Data Based on Graph Structure

一种基于图结构的表达数据聚类方法

• 发表时间: 2004
• 期刊: Genome Informatics 15・2
• 作者: S.Seno;R.Teramoto;Y.Takenaka;H.Matsuda
• 通讯作者: H.Matsuda

An OGSA-based Integration of Life Science Resources

基于OGSA的生命科学资源整合

• 发表时间: 2005
• 期刊: Methods of Information in Medicine 44(2)
• 作者: Kosaka;T.
• 通讯作者: T.

Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics

具有位置透明性的生物信息学网格研究平台的架构

• 发表时间: 2005
• 期刊: Lecture Notes in Bioinformatics 3370
• 作者: Y.Tohsato;T.Kosaka;S.Date;S.Shimojo;H.Matsuda
• 通讯作者: H.Matsuda

Haruki Nakamura, et al.: "A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science"New Generation Computing. 22・2. 157-166 (2004)

Haruki Nakamura 等：“对先进生命科学的下一代研究基础设施的挑战”新一代计算 157-166。

Development of a database system for drug discovery by employing grid technology

利用网格技术开发药物发现数据库系统

• 发表时间: 2004
• 期刊: Information Technology Letters 3
• 作者: K.Taki;R.Teramoto;Y.Takenaka;H.Matsuda
• 通讯作者: H.Matsuda