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Hybrid data mining for discovery of knowledge about protein functions

Research Project

Project/Area Number 21500139
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Intelligent informatics
Research InstitutionKobe University

Principal Investigator

OHKAWA Takenao  神戸大学, 大学院・システム情報学研究科, 教授 (30223738)

Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2010: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2009: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords知識発見 / データマイニング / バイオインフォマティクス / バイオデータ処理 / 情報抽出
Research Abstract

Several methods for hybrid data mining from the various types of data such as the protein 3D structure data, the network data(e. g. protein-protein interaction data and metabolic pathways), and the text data describing the results of the protein structure analysis have been proposed. Applications to the knowledge discovery of protein functions, which include prediction of the protein functional sites, information extraction from the biomedical articles, retrieval of similar articles considering user's aspect, and classification of organisms from the viewpoint of the biological function, have been developed based on the proposed data mining methods.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (30 results)

All 2011 2010 2009 Other

All Journal Article (12 results) (of which Peer Reviewed: 12 results) Presentation (18 results)

  • [Journal Article] Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks2011

    • Author(s)
      Hiroyuki Monji, Satoshi Koizumi, Tomonobu Ozaki, and Takenao Ohkawa
    • Journal Title

      BMC Bioinformatics

      Volume: Vol.12(Suppl 1)

    • NAID

      40017032110

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] A method for supporting retrieval of articles on protein structure analysis considering users' intention2011

    • Author(s)
      Riku Kyogoku, Ryo Fujimoto, Tomonobu Ozaki, and Takenao Ohkawa
    • Journal Title

      BMC Bioinformatics

      Volume: Vol.12(Suppl 1)

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] 定量的アイテム集合付き単一グラフからの頻出パターンマイニング2011

    • Author(s)
      三好裕樹, 尾崎知伸, 江口浩二, 大川剛直
    • Journal Title

      人工知能学会論文誌

      Volume: Vol.26, No.1 Pages: 284-296

    • NAID

      130000455377

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A method to extract sentences containing protein function information with training data extension based on user's feedback2010

    • Author(s)
      Kazunori Miyanishi, Tomonobu Ozaki, and Takenao Ohkawa
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: Vol.3 Pages: 82-90

    • NAID

      130000418487

    • Related Report
      2011 Final Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Method to identify protein names with iterative extension of training data set2010

    • Author(s)
      Kazunori Miyanishi, Tomonobu Ozaki, and Takenao Ohkawa
    • Journal Title

      Proceedings of the 2nd International Conference on Bioinformatics and Computational Biology(BICoB-2010)

      Pages: 178-183

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] 内部および外部重みを考慮した頻出部分グラフマイニング2010

    • Author(s)
      信田正樹, 尾崎知伸, 大川剛直
    • Journal Title

      情報処理学会論文誌:データベース

      Volume: Vol.3, No.2 Pages: 1-12

    • NAID

      110007990078

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A comparative analysis of metabolic pathways based on metabolic steady states2009

    • Author(s)
      Yuta Ashida, Tomonobu Ozaki, and Takenao Ohkawa
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: Vol.2, No.4 Pages: 83-92

    • NAID

      130000140292

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Selection of effective sentences from a corpus to improve the accuracy of identification of protein names2009

    • Author(s)
      Kazunori Miyanishi, Tomonobu Ozaki, and Takenao Ohkawa
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: Vol.2, No.4 Pages: 93-100

    • NAID

      130000140293

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Comparative Analysis of Metabolic Pathways Based on Metabolic Steady States2009

    • Author(s)
      Yuta Ashida, Tomonobu Ozaki, Takenao Ohkawa
    • Journal Title

      IPSJ Transactions on Bioinformatics Vol.2, No.4

      Pages: 83-92

    • NAID

      130000140292

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Selection of Effective Sentences from a Corpus to Improve the Accuracy of Identification of Protein Names2009

    • Author(s)
      Kazunori Miyanishi, Tomonobu Ozaki, Takenao Ohkawa
    • Journal Title

      IPSJ Transactions on Bioinformatics Vol.2, No.4

      Pages: 93-100

    • NAID

      130000140293

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 複合構造グラフからの頻出強相関パターン発見2009

    • Author(s)
      山本翼, 三好裕樹, 尾崎知伸, 大川剛直
    • Journal Title

      情報処理学会論文誌:データベース Vol.2, No.3

      Pages: 53-66

    • NAID

      110007990054

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A method of extracting sentences containing protein function information from articles by iterative learning with feature update

    • Author(s)
      Kazunori Miyanishi and Takenao Ohkawa
    • Journal Title

      Proceedings of the Ninth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics

      Pages: 10-10

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Presentation] 文の接続関係を考慮した蛋白質構造解析文献からの相互作用記述文抽出方法2011

    • Author(s)
      京極陸, 大川剛直
    • Organizer
      情報処理学会,第25回バイオ情報学研究会
    • Place of Presentation
      琉球大学
    • Related Report
      2011 Final Research Report
  • [Presentation] タンパク質の立体構造情報と類似部分グラフマイニングを利用した結合部位の自動抽出に関する研究2011

    • Author(s)
      文字宏之, 大川剛直
    • Organizer
      情報処理学会,第25回バイオ情報学研究会
    • Place of Presentation
      琉球大学
    • Related Report
      2011 Final Research Report
  • [Presentation] 利用者の意図を考慮した概念的観点に基づく蛋白質構造解析文献検索手法2011

    • Author(s)
      麻生知希, 大川剛直
    • Organizer
      情報処理学会,第25回バイオ情報学研究会
    • Place of Presentation
      琉球大学
    • Related Report
      2011 Final Research Report
  • [Presentation] 文の接続関係を考慮した蛋白質構造解析文献からの相互作用記述文抽出方法2011

    • Author(s)
      京極陸, 大川剛直
    • Organizer
      情報処理学会第25回バイオ時報学研究会
    • Place of Presentation
      琉球大学
    • Related Report
      2011 Annual Research Report
  • [Presentation] タンパク質の立体構造情報と類似部分グラフマイニングを利用した結合部位の自動抽出に関する研究2011

    • Author(s)
      文字宏之, 大川剛直
    • Organizer
      情報処理学会第25回バイオ情報学研究会
    • Place of Presentation
      琉球大学
    • Related Report
      2011 Annual Research Report
  • [Presentation] 利用者の意図を考慮した概念的観点に基づく蛋白質構造解析文献検索手法2011

    • Author(s)
      麻生知希, 大川剛直
    • Organizer
      情報処理学会第25回バイオ情報学研究会
    • Place of Presentation
      琉球大学
    • Related Report
      2011 Annual Research Report
  • [Presentation] Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks2011

    • Author(s)
      Hiroyuki Monji, Satoshi Koizumi, Tomonobu Ozaki, Takenao Ohkawa
    • Organizer
      The 9th Asia-Pacific Bioinformatics Conference
    • Place of Presentation
      Songdo Convensia, Incheon, (Korea)
    • Related Report
      2010 Annual Research Report
  • [Presentation] A method for supporting retrieval of articles on protein structure analysis considering users' intention2011

    • Author(s)
      Riku Kyogoku, Ryo Fujimoto, Tomonobu Ozaki, Takenao Ohkawa
    • Organizer
      The 9th Asia-Pacific Bioinformatics Conference
    • Place of Presentation
      Songdo Convensia, Incheon, (Korea)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Mining interesting patterns and rules in a time-evolving graph2011

    • Author(s)
      Yuuki Miyoshi, Tomonobu Ozaki, Takenao Ohkawa
    • Organizer
      International Conference on Data Mining and Applications
    • Place of Presentation
      The Royal Garden Hotel, Kowloon, (Hong Kong)
    • Related Report
      2010 Annual Research Report
  • [Presentation] ユーザフィードバックに基づく訓練データ拡張を伴う蛋白質機能情報文抽出に関する研究2010

    • Author(s)
      宮西一徳, 尾崎知伸, 大川剛直
    • Organizer
      情報処理学会,第23回バイオ情報学研究会
    • Place of Presentation
      九州大学
    • Related Report
      2011 Final Research Report
  • [Presentation] 蛋白質-蛋白質相互作用ネットワークにおける周辺クラスタとの立体構造類似度を考慮した相互作用部位予測2010

    • Author(s)
      小泉敏史, 尾崎知伸, 大川剛直
    • Organizer
      人工知能学会,第77回人工知能基本問題研究会
    • Place of Presentation
      北海道大学
    • Related Report
      2011 Final Research Report
  • [Presentation] 概念的類似度の更新に基づく観点を考慮した蛋白質構造解析文献の検索支援2010

    • Author(s)
      藤本亮, 尾崎知伸, 大川剛直
    • Organizer
      人工知能学会,第77回人工知能基本問題研究会
    • Place of Presentation
      北海道大学
    • Related Report
      2011 Final Research Report
  • [Presentation] ユーザフィードバックに基づく訓練データ拡張を伴う蛋白質機能情報文抽出に関する研究2010

    • Author(s)
      宮西一徳, 尾崎知伸, 大川剛直
    • Organizer
      情報処理学会第23回バイオ情報学研究会
    • Place of Presentation
      九州大学伊都キャンパス総合学習プラザ
    • Related Report
      2010 Annual Research Report
  • [Presentation] A Method to Identify Protein Names with Iterative Extension of Training Data Set2010

    • Author(s)
      宮西一徳, 尾崎知伸, 大川剛直
    • Organizer
      2nd International Conference on Bioinformatics and Computational Biology
    • Place of Presentation
      Sheraton Waikiki Hotel(USA)
    • Related Report
      2009 Annual Research Report
  • [Presentation] 蛋白質-蛋白質相互作用ネットワークにおける周辺クラスタとの立体構造類似度を考慮した相互作用部位予測2010

    • Author(s)
      小泉敏史, 尾崎知伸, 大川剛直
    • Organizer
      人工知能学会 第77回 人工知能基本問題研究会
    • Place of Presentation
      北海道大学(北海道)
    • Related Report
      2009 Annual Research Report
  • [Presentation] 概念的類似度の更新に基づく観点を考慮した蛋白質構造解析文献の検索支援2010

    • Author(s)
      藤本亮, 尾崎知伸, 大川剛直
    • Organizer
      人工知能学会 第77回 人工知能基本問題研究会
    • Place of Presentation
      北海道大学(北海道)
    • Related Report
      2009 Annual Research Report
  • [Presentation] コーパスからの文選択による事例集合拡張に基づく蛋白質名判定2009

    • Author(s)
      宮西一徳, 尾崎知伸, 大川剛直
    • Organizer
      情報処理学会,第19回バイオ情報学研究会
    • Place of Presentation
      電気通信大学
    • Related Report
      2011 Final Research Report
  • [Presentation] コーパスからの文選択による事例集合拡張に基づく蛋白質名判定2009

    • Author(s)
      宮西一徳, 尾崎知伸, 大川剛直
    • Organizer
      情報処理学会 第19回バイオ情報学研究会
    • Place of Presentation
      電気通信大学(東京都)
    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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