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2009 Fiscal Year Final Research Report

Reconstruction and Analysis of Life Systems Using Knowledge-Processing Technology

Research Project

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Project/Area Number 17017002
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

TAKAGI Toshihisa  The University of Tokyo, 大学院・新領域創成科学研究科, 教授 (30110836)

Co-Investigator(Kenkyū-buntansha) TSUJII Junichi  東京大学, 大学院・情報理工学系研究科, 教授 (20026313)
NAKAYA Akihiro  東京大学, 大学院・新領域創成科学研究科, 准教授 (60301149)
IWASAKI Wataru  東京大学, 大学院新領域創成科学研究科, 助教 (50545019)
Project Period (FY) 2005 – 2009
Keywordsオントロジー / 機能解析 / パスウェイデータベース / テキストからの情報抽出 / 自然言語処理 / QTL解析 / 知識発見 / 文献クラスタリング
Research Abstract

To understand life as systems, we developed the following technologies: high-dimensional QTL analysis by using abundant image data, interpretation of omics experiments assisted by text-mining, text mining of methodological information from literatures, classification of figures in research papers, evolutionary analysis of genomes and biological networks by using abundant genome data, methods for comparing networks from different species, and navigation tools for interpreting huge network data.

  • Research Products

    (31 results)

All 2009 2008 2007 2006 2005 Other

All Journal Article (13 results) Presentation (7 results) Book (1 results) Remarks (10 results)

  • [Journal Article] Classifying biomedical figures using combination of bag of keypoints and bag of keywords, Proc. of 2nd Int. Workshop on Intell2009

    • Author(s)
      Koike, A., Takagi, T.
    • Journal Title

      Inform. in Biol. and Med.

      Pages: 848-853

  • [Journal Article] Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages2009

    • Author(s)
      Iwasaki, W., Takagi, T.
    • Journal Title

      PLoS Genetics. 5(3)

      Pages: e1000402

  • [Journal Article] Figure Classification in Biomedical Literature towards Figure Mining2008

    • Author(s)
      Ishii, N., Koike, A., Yamamoto, Y., Takagi, T.
    • Journal Title

      IEEE International Conference on Bioinformatics and Biomedicine

      Pages: 263-269

  • [Journal Article] Reconstruction of Highly Heterogeneous Gene-Content Evolution across the Three Domains of Life2007

    • Author(s)
      Iwasaki, W., Takagi, T.
    • Journal Title

      Bioinformatics (ISMB/ECCB2007 proceeding issue) 23

      Pages: i230-i239

  • [Journal Article] OReFiL: an online resource finder for life sciences2007

    • Author(s)
      Yamamoto, Y., Takagi, T.
    • Journal Title

      BMC Bioinformatics 8

      Pages: 287

  • [Journal Article] Biomedical knowledge navigation by literature clustering2007

    • Author(s)
      Yamamoto, Y., Takagi, T.
    • Journal Title

      Journal of Biomedical Informatics 40(2)

      Pages: 114-130

  • [Journal Article] Knowledge discovery based on an implicit and explicit conceptual network.2007

    • Author(s)
      Koike, A., Takagi, T.
    • Journal Title

      J. Am. Soc. Info. Sci. Tech. 58(1)

      Pages: 51-65

  • [Journal Article] Improving the performance of an SVM-based method for predicting protein-protein interactions2006

    • Author(s)
      Dohkan, S., Koike, A., Takagi, T.
    • Journal Title

      In Silico Biol. 6

      Pages: 0048

  • [Journal Article] MetaGene: prokaryotic gene finding from environmental genome shotgun sequences2006

    • Author(s)
      Noguchi, H., Park, J., Takagi, T.
    • Journal Title

      Nucleic Acids Res. 34(19)

      Pages: 5623-5630

  • [Journal Article] ALICE: An Algorithm to Extract Abbreviations from MEDLINE2005

    • Author(s)
      Ao, H., Takagi, T.
    • Journal Title

      JAMIA 12(5)

      Pages: 576-586

  • [Journal Article] Automatic Extraction of Gene/protein Biological Functions from Biomedical Text2005

    • Author(s)
      Koike, A., Niwa, Y., Takagi, T.
    • Journal Title

      Bioinformatics 21

      Pages: 1227-1236

  • [Journal Article] Biomedical Information Extraction with Predicate-Argument Structure Patterns, Proc2005

    • Author(s)
      Yakushiji, A., Miyao, Y., Tateisi, Y., Tsujii, J.
    • Journal Title

      1st Int. Symp. on Semantic Mining in Biomedicine

      Pages: 60-69

  • [Journal Article] Syntax Annotation for the GENIA corpus, Proc2005

    • Author(s)
      Tateisi, Y., Yakushiji, A., Ohta, T., Tsujii, J.
    • Journal Title

      IJCNLP 2005

      Pages: 222-227

  • [Presentation] Effective multi-scale graph navigation system powered by fast and biologically meaningful hierarchical clustering2009

    • Author(s)
      Praneenararat, T. (Takagi, T. )
    • Organizer
      GIW2009
    • Place of Presentation
      横浜
    • Year and Date
      20091214-20091216
  • [Presentation] Biomedical figure search using combination of bag of keypoints and bag of words2009

    • Author(s)
      Koike, A. (Takagi, T. )
    • Organizer
      GIW2009
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-15
  • [Presentation] Classification of neuroimaging figures toward automatic figure annotation system2009

    • Author(s)
      Ishii, N. (Takagi, T. )
    • Organizer
      GIW2009
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-14
  • [Presentation] 生命科学研究者のための統合文献情報管理システム2009

    • Author(s)
      岩崎渉
    • Organizer
      第32回日本分子生物学会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-10
  • [Presentation] メダカ顔貌形状に関わる遺伝子座の探索に向けた量的形質の定量手法2009

    • Author(s)
      鈴志野康正(中谷明弘)
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-09
  • [Presentation] Reconstruction of highly heterogeneous gene-content evolution across the three domains of life2007

    • Author(s)
      Iwasaki, W.
    • Organizer
      ISMB/ECCB2007
    • Place of Presentation
      Wien
    • Year and Date
      2007-07-24
  • [Presentation] A prototype platform for flexible comparison analyses of interactions and pathways2007

    • Author(s)
      Fukagawa, H. (Takagi, T. )
    • Organizer
      ISMB/ECCB2007
    • Place of Presentation
      Wien
    • Year and Date
      2007-07-22
  • [Book] 医学生物学分野におけるシソーラスとテキストマイニング技術の開発(実験医学増刊号)2008

    • Author(s)
      小池麻子(高木利久)
    • Total Pages
      6
    • Publisher
      羊土社
  • [Remarks] MCTDB: Medaka Craniofacial Trait Database

    • URL

      http://medaka.cb.k.u-tokyo.ac.jp/mctdb/

  • [Remarks] BioTermNet

    • URL

      http://btn.ontology.ims.u-tokyo.ac.jp/

  • [Remarks] OReFiL

    • URL

      http://orefil.dbcls.jp/

  • [Remarks] PIPS

    • URL

      http://prime.ontology.ims.u-tokyo.ac.jp:8081/cgi-bin/PIPS.cgi

  • [Remarks] McSyBi

    • URL

      http://textlens.hgc.jp/McSyBi/index.html

  • [Remarks] GENA

    • URL

      http://gena.ontology.ims.u-tokyo.ac.jp:8081/search

  • [Remarks] Multiple Ontology Viewer

    • URL

      http://gena.ontology.ims.u-tokyo.ac.jp:8081/mov

  • [Remarks] MEDLINE全体のテキストをEnjuで解析した結果。リクエスト先メールアドレス

  • [Remarks] GENIA Treebank

    • URL

      http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/topics/Corpus/GTB.html

  • [Remarks] ALICE

    • URL

      http://uvdb3.hgc.jp/ALICE/ALICE_index.html

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Published: 2011-06-18   Modified: 2017-10-17  

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