Statistical method to represent biomedical knowledge

• Project/Area Number: 17017037
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Genetics
• Principal Investigator: OKUBO Kousaku National Institute of Genetics, 生命情報・DDBJ研究センター, 教授 (40233069)
• Project Period (FY): 2005 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥62,300,000 (Direct Cost: ¥62,300,000); Fiscal Year 2009: ¥12,900,000 (Direct Cost: ¥12,900,000); Fiscal Year 2008: ¥12,700,000 (Direct Cost: ¥12,700,000); Fiscal Year 2007: ¥12,500,000 (Direct Cost: ¥12,500,000); Fiscal Year 2006: ¥12,400,000 (Direct Cost: ¥12,400,000); Fiscal Year 2005: ¥11,800,000 (Direct Cost: ¥11,800,000)
• Keywords: ゲノム / 情報工学 / マイクロアレイ / 遺伝子 / 生体生命情報学

Research Abstract

On assumption that "the distribution of 1) technical terms and 2) enlisted topics in a Textbook" is a measurable representation of a domain knowledge, We have applied latent semantic indexing technique to the index section of a textbook to make a vector space of words and pages.
In this space, the semantic relation of terms and topics are expected to be represented by the cosine between the term vectors as well as page vectors. The authenticity, sensitivity and specificity of the resulted space was psychologically tested by applying interpretation of gene orders took from genome, expression clusters, as well as in adhoc clustering of PubMed abstracts retrieved by a common key word .
Quantitative evaluation of the results which is essential for tuning parameters is a problem still left behind.

Research Products

• [Journal Article] On theoretical models of gene expression evolution with random genetic drift and natural selection (2009)
  • Author(s): Ogasawara O., Okubo K.
  • Journal Title: PLoS One. 4(11)
• [Journal Article] On theoretical models of gene expression evolution with random genetic drift and natural selection (2009)
  • Author(s): Ogasawara O.
  • Journal Title: PLoS One 4巻11号
  • Peer Reviewed
• [Journal Article] Cornichon-like Protein Facilitates Secretion of HB-EGF and Regulates Proper Development of CranialNerves. (2007)
  • Author(s): Hoshino H, Uchida T, Otsuki T, Kawamoto S, Okubo K, Takeichi M, Chisaka O.
  • Journal Title: Molecular Biology of the Cell Apr Vol.18
• [Journal Article] Cornichon-like Protein Facilitates Secretion of HB-EGF and Regulates Proper Development of Cranial Nerves. (2007)
  • Author(s): Chisaka O
  • Journal Title: Molecular Biology of the Cell. 18 Pages: 1143-1152
• [Journal Article] BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. (2006)
  • Author(s): Ogasawara O, Otsuji M, Watanabe K, Iizuka T, Tamura T, Hishiki T, Kawamoto S, Okubo K.
  • Journal Title: Nucleic Acids Res 34
• [Journal Article] BodyMap-Xs : anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. (2006)
  • Author(s): Ogasawara O
  • Journal Title: Nucleic Acids Res. 34(Database issue) Pages: 628-631
• [Journal Article] DDBJ in preparation for overview of research activities behind data submissions. (2006)
  • Author(s): Okubo K
  • Journal Title: Nucleic Acids Res. 34(Database issue) Pages: 6-9
• [Journal Article] Identification of differentially expressed genes in psoriasis using expression profiling approaches. (2005)
  • Author(s): Itoh K, Kawasaki S, Kawamoto S, Seishima M, Chiba H, Michibata H, Wakimoto K, Imai Y, Minesaki Y, Otsuji M, Okubo K.
  • Journal Title: Exp Dermatol. 14(9) Pages: 667-74
• [Journal Article] Quantification of gene expression in mouse and human renal proximal tubules (2005)
  • Author(s): Kaimori JY, Takenaka M, Okubo K.
  • Journal Title: Methods Mol Biol. 293 Pages: 209-19
• [Journal Article] The Human Anatomic Gene Expression Library (H-ANGEL) (2005)
  • Author(s): Tanino, M., Debily, MA., Tamura, T., Hishiki, T., Ogasawara, O., Murakawa, K., Kawamoto, S., Itoh, K., Watanabe, S., de Souza, SJ., Imbeaud, S., Graudens, E., Eveno, E., Hilton, P., Sudo, Y., Kelso, J., Ikeo, K., Imanishi, T., Gojobori, T., Auffray, C., Hide, W., Okubo K
  • Journal Title: Nucleic Acids Res 33
• [Journal Article] Identification of differentially expressed genes in psoriasis using expression profiling approaches. (2005)
  • Author(s): Itoh K
  • Journal Title: Exp Dermatol. 9 Pages: 667-674
• [Journal Article] Quantification of gene expression in mouse and human renal proximal tubules. (2005)
  • Author(s): Kaimori JY
  • Journal Title: Methods Mol Biol. 293 Pages: 209-219
• [Journal Article] DDBJ in collaboration with mass-sequencing teams on annotation. (2005)
  • Author(s): Tateno, Y.
  • Journal Title: Nucleic Acids Res. 33(Database Issue)
• [Journal Article] The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. (2005)
  • Author(s): Tanino, M.
  • Journal Title: Nucleic Acids Res. 33(Database Issue)
• [Journal Article] ポストゲノム時代に高まるバイオ自然言語処理への期待:バイオ自然言語処理最新事情5.ゲノムデータの機械解釈 (2005)
  • Author(s): 大久保 公策
  • Journal Title: 情報処理 46・2480 Pages: 137-142
  • NAID: 110002768351
• [Presentation] 科学を社会に役立てるには (2008)
  • Author(s): 大久保公策
  • Organizer: (独)日本学術振興会ゲノムテクノロジー第164委員会第27回研究会
  • Place of Presentation: 東京大学山上会館
  • Year and Date: 2008-07-22
• [Presentation] 生命科学分野でのDB統合の意味と意義 (2007)
  • Author(s): 大久保公策
  • Organizer: 日本バイオインフォマティクス学会第1回JSBi合同研究会
  • Place of Presentation: 東京大学医科学研究所
  • Year and Date: 2007-05-29
• [Book] 「生命科学データベースの現状と課題」 (2007)
  • Author(s): 大久保公策
  • Total Pages: 5
  • Publisher: 株式会社岩波書店
• [Book] 文献知識の計算機による利用がなぜ必要か (2005)
  • Author(s): 大久保 公策
  • Publisher: 共立出版株式会社
• [Remarks] BOB(試験公開サーバー)
  • URL: http://222.151.240.6/project/bob/080208-/simple.cgi
• [Remarks] CGED Source Classification Database
  • URL: http://cged.genes.nig.ac.jp/scd/
• [Remarks] H-Angel
  • URL: http://www.jbirc.aist.go.jp/hinv/h-angel/wge.top
• [Remarks] BodyMap-Xs
  • URL: http://bodymap.jp
• [Remarks] BOB(試験公開サーバー)ユーザ制限あるためにパスワード設定中
  • URL: http://222.151.240.6/project/bob/080208-/simple.cgi