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Construction of Federated Genome Knowledgebases by Grid Computing

Research Project

Project/Area Number 15607013
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field 計算科学
Research InstitutionOsaka University

Principal Investigator

MATSUDA Hideo  Osaka University, Graduate School of Information Science and Technology, Professor, 大学院・情報科学研究科, 教授 (50183950)

Co-Investigator(Kenkyū-buntansha) DATE Susumu  Osaka University, Graduate School of Information Science and Technology, Assistant Professor, 大学院・情報科学研究科, 助手 (20346175)
Project Period (FY) 2003 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥3,500,000 (Direct Cost: ¥3,500,000)
Fiscal Year 2004: ¥1,700,000 (Direct Cost: ¥1,700,000)
Fiscal Year 2003: ¥1,800,000 (Direct Cost: ¥1,800,000)
KeywordsGrid 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
Research Abstract

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.

Report

(3 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • Research Products

    (15 results)

All 2005 2004 Other

All Journal Article (12 results) Publications (3 results)

  • [Journal Article] An OGSA-based Integration of Life Science Resources2005

    • Author(s)
      T.Kosaka, Y.Tohsato, S.Date, H.Matsuda, S.Shimojo
    • Journal Title

      Methods of Information in Medicine 44・2(in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Heterogeneous Database Federation using Grid Technology for Drug Discovery Process2005

    • Author(s)
      Y.Tohsato, T.Kosaka, S.Date, S.Shimojo, H.Matsuda
    • Journal Title

      Lecture Notes in Bioinformatics 3370

      Pages: 43-52

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] An OGSA-based Integration of Life Science Resources2005

    • Author(s)
      T.Kosaka, Y.Tohsato, S.Date, H.Matsuda, S.Shimojo
    • Journal Title

      Methods of Information in Medicine 44-2 (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics2005

    • Author(s)
      Y.Tohsato, T.Kosaka, S.Date, S.Shimojo, H.Matsuda
    • Journal Title

      Lecture Notes in Bioinformatics 3370

      Pages: 43-52

    • NAID

      130003997344

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics2004

    • Author(s)
      Y.Kido, S.Date, S.Takeda, S.Hatano, J.Ma, S.Shimojo, H.Matsuda
    • Journal Title

      Genome Informatics 15・2

      Pages: 3-12

    • NAID

      130003997344

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] A Method for Clustering Expression Data Based on Graph Structure2004

    • Author(s)
      S.Seno, R.Teramoto, Y.Takenaka, H.Matsuda
    • Journal Title

      Genome Informatics 15・2

      Pages: 151-160

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] 遺伝子の機能分類を利用した遺伝子制御ネットワーク推定手法2004

    • Author(s)
      瀧浩平, 寺本礼仁, 竹中要一, 松田秀雄
    • Journal Title

      情報科学技術レターズ 3

      Pages: 23-24

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Biased biological functions of horizontally transferred genes in prokaryotic genomes2004

    • Author(s)
      Y.Nakamura, T.Itoh, H.Matsuda, T.Gojobori
    • Journal Title

      Nature Genetics 36・7

      Pages: 760-766

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics2004

    • Author(s)
      Y.Kido, S.Date, S.Takeda, S.Hatano, J.Ma, S.Shimojo, H.Matsuda
    • Journal Title

      Genome Informatics 15-2

      Pages: 3-12

    • NAID

      130003997344

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] A Method for Clustering Expression Data Based on Graph Structure2004

    • Author(s)
      S.Seno, R.Teramoto, Y.Takenaka, H.Matsuda
    • Journal Title

      Genome Informatics 15-2

      Pages: 151-160

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Development of a database system for drug discovery by employing grid technology2004

    • Author(s)
      K.Taki, R.Teramoto, Y.Takenaka, H.Matsuda
    • Journal Title

      Information Technology Letters 3

      Pages: 365-369

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Biased biological functions of horizontally transferred genes in prokaryotic genomes2004

    • Author(s)
      Y.Nakamura, T.Itoh, H.Matsuda, T.Gojobori
    • Journal Title

      Nature Genetics 36-7

      Pages: 760-766

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Publications] Haruki Nakamura, et al.: "A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science"New Generation Computing. 22・2. 157-166 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hideo Matsuda: "Bridging Life Science Databases with Globus 3/OGSA-DAI for Supporting Drug Discovery"Globus World. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yusuke Saito, et al.: "Real-Time Mapping System of cDNAs and Genomes using Grid Computing"Genome Informatics. 14. (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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