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Construction and Retrieval of Highly Integrated Biological Databases

Research Project

Project/Area Number 12208007
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

GOTO Susumu  Kyoto University, Institute for Chemical Research, Associate Professor, 化学研究所, 助教授 (40263149)

Co-Investigator(Kenkyū-buntansha) AKUTSU Tatsuya  Kyoto University, Institute for Chemical Research, Professor, 化学研究所, 教授 (90261859)
SATOU Kenji  Japan Advanced Institute of Science and Technology, School of Knowledge Science, Associate Professor, 知識科学研究科, 助教授 (10215783)
HATTORI Masahiro  Kyoto University, Institute for Chemical Research, Instructor, 化学研究所, 助手 (60372554)
OKUNO Yasushi  Kyoto University, Institute for Chemical Research, Instructor, 化学研究所, 助手 (20283666)
Project Period (FY) 2000 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥91,900,000 (Direct Cost: ¥91,900,000)
Fiscal Year 2004: ¥17,600,000 (Direct Cost: ¥17,600,000)
Fiscal Year 2003: ¥18,000,000 (Direct Cost: ¥18,000,000)
Fiscal Year 2002: ¥30,800,000 (Direct Cost: ¥30,800,000)
Fiscal Year 2001: ¥25,500,000 (Direct Cost: ¥25,500,000)
KeywordsDatabase / Bioinformatics / Ontology / Algorithm / Molecular interaction / Reaction network / GRID / Network topology / 化合物構造比較 / 糖鎖構造データベース / グラフトポロジー / 統合データベース / タンパク質立体構造予測 / 文献からの知識抽出 / タンパク質間相互作用予測 / グリッドコンピューティング / 分子生物学データベース / 酵素反応 / グラフ比較 / 相関クラスタ / 経路探索 / アミノ酸配列類似度データ / リンク情報 / 相関ルール発見手法 / ゲノムデータベース / 知識抽出 / マイクロアレイ発現データ
Research Abstract

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 database
We 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 databases
We 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 topologies
We 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

Report

(6 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (37 results)

All 2005 2004 Other

All Journal Article (13 results) Publications (24 results)

  • [Journal Article] Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature2005

    • Author(s)
      Satou, K. et al.
    • Journal Title

      In silico Biology 5

      Pages: 67-69

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] An integrated system for distributed bioinformatics environment on grids2005

    • Author(s)
      Satou, K. et al.
    • Journal Title

      Grid Computer in Life Science (Lecture Notes in Bioinformatics) 3370

      Pages: 8-19

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Fast and accurate database homology search using upper bounds of local alignment scores2005

    • Author(s)
      Itoh, M. et al.
    • Journal Title

      Bioinformatics 21

      Pages: 912-921

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Two complementary representation of a scale-free network2005

    • Author(s)
      Nacher, J.C. et al.
    • Journal Title

      Physica A 349

      Pages: 349-363

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Two complementary representation of a scale-free network2005

    • Author(s)
      Nacher J.C.et al.
    • Journal Title

      Physica A 349

      Pages: 349-363

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Fast and accurate database homology search using upper bounds of local alignment2005

    • Author(s)
      Itoh, M., Goto, S., Akutsu, T., Kanehisa, M.
    • Journal Title

      Bioinformatics 21

      Pages: 912-921

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Two complementary representations of a scale-free network2005

    • Author(s)
      Nacher, J.C., Yamada, T., Goto, S., Kanehisa, M., Akutsu, T.
    • Journal Title

      Physica A 349

      Pages: 349-363

    • Related Report
      2004 Annual Research Report
  • [Journal Article] The KEGG resource for deciphering the genome2004

    • Author(s)
      Kanehisa, M. et al.
    • Journal Title

      Nucleic Acids Research 32

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions2004

    • Author(s)
      Kotera, M. et al.
    • Journal Title

      Journal of American Chemical Society 126

      Pages: 16487-16498

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions2004

    • Author(s)
      Kotera, M., Okuno, Y., Hattori, M., Goto, S., Kanehisa, M.
    • Journal Title

      J.Am.Chem.Soc. 126

      Pages: 16487-16498

    • Related Report
      2004 Annual Research Report
  • [Journal Article] KCaM (KEGG Carbohydrate Matcher) : a software tool for analyzing the structures of carbohydrate sugar chains2004

    • Author(s)
      Aoki, K.F., et al.
    • Journal Title

      Nucleic Acids Res. 32

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Extraction of phylogenetic network modules from prokaryote Metabokic pathways2004

    • Author(s)
      Yamada, T., Goto, S., Kanehisa, M.
    • Journal Title

      Genome Informatics 15

      Pages: 249-259

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature2004

    • Author(s)
      Satou, K., Yamamoto, K.
    • Journal Title

      In Silico Biology 5

      Pages: 8-8

    • Related Report
      2004 Annual Research Report
  • [Publications] Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: "The KEGG resource for deciphering genome"Nucleic Acids Research. 32. D277-D280 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hattori, M., Okuno, Y., Goto, S., Kanehisa, M.: "Development of a chemical comparison method for integrated analysis of chemical and genomic information in the metabolic pathways"Journal of the American Chemical Society. 125. 11853-11865 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hayashida, M., Ueda, N., Akutsu, T.: "Inferring strength of protein-protein interactions from experimental data using linear programming"Bioinformatics. 19. ii58-ii65 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Akutsu, T.: "Efficient extraction of mapping rules of atoms from enzymatic reaction data"Proceedings of the 7th International Conference of Computational Molecular Biology. 1-8 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Pham, T.H., Satou, K., Ho, T.B.: "Prediction and analysis of β-turns in proteins by support vector machine"Genome Informatics. 14. 196-205 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Clemente Litran, J.C., Defago, X, Satou, K.: "Asynchronous peer-to-peer communication for failure resilient distributed genetic algorithms"Proceedings of the 15th IASTED International Conference on Parallel and Distributed Computing. 2. 769-773 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Satou, K., Defago, X., Yamamoto, T., Konagaya, A.: "STAG : A system for integrated search and data mining for bioinformatics"CBI Journal. (In press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Oyama, T., Kitano, K., Satou, K., Ito, T.: "Extraction of knowledge on protein-protein interaction by association rule discovery"Bioinformatics. 18・5. 705-714 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Dukka, B.K.C., Akutsu, T., Tomita, E., Seki, T., Fujiyama, A.: "Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm"Genome Informatics. 13. 143-152 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Akutsu, T., Bannai, H., Miyano, S., Ott, S.: "On the complexity of deriving position specific score matrices from examples"Lecture Notes in Computer Science. 2372. 168-177 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Akutsu, T., Ott, S.: "Inferring a union of halfspaces from examples"Lecture Notes in Computer Science. 2387. 117-126 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yamada, T., Yamanishi, Y., Goto, S., Kanehisa, M.: "Extraction of modules from metabolic pathways with phylogenetic profile"Genome Informatics. 13. 353-354 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Goto, S., +4: "LIGAND : database of chemical compounds and reactions in biological pathways"Nucleic Acids Research. 30. 402-404 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Kanehisa, M., Goto, S., Kawashima, S., Nakaya, A.: "The KEGG database at GenomeNet"Nucleic Acids Research. 30. 42-46 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Nakay, A., Goto, S., Kanehisa, M.: "Extraction of correlated gene clusters by multiple graph comparison"Genome Informatics. 12. 44-53 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Satou, K., Fuseda, Y., Konagaya, A., Takagi, T.: "A framework for quick-and-pinpoint data mlning and its application to heterogeneous genome databases"Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies (KES2001). 1. 773-777 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Kuroda, M., +35: "Whole genome sequencing of meticillin-resistant Staphylococcus aureus"Lancet. 357. 1225-1240 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Sato, Y., +5: "SSDB : sequence similarity database in KEGG"Genome Informatics. 12. 230-231 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Goto,S.,Kawashima,S.,Okuji,Y,Kamiya,T.,Miyazaki,S.,+2: "KEGG/EXPRESSION : A database for browsing and analysing microarray expression data."Genome Informatics. 11. 222-223 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Nakaya,A.,Gate,S.and Kanehisa,M.: "Extraction of correlated gene clusters from multiple graph structures : Theory."Genome Informatics. 11. 270-271 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kawashima,S.,Nakaya,A.,Okuji,Y.,Goto,S.and Kanehisa,M.: "Extraction of correlated gene clusters from multiple graph structures : Application."Genome Informatics. 11. 272-273 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ogata,H.,Fujibuchi,W.,Goto,S.and Kanehisa,M.: "A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters."Nucleic Acids Research. 28. 4021-4028 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Yagyuu,T.and Satou,K.: "Toward automatic construction of extensional ontology from genome databases."Genome Informatics. 11. 442-443 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Naitou,T.,Satou,K.,Furuichi,E.,Kuhara,S.and Takagi,T.: "A system for finding association rules from microarray data and public databases."Genome Informatics. 11. 356-357 (2000)

    • Related Report
      2000 Annual Research Report

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Published: 2001-04-01   Modified: 2018-03-28  

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