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Development of both the data exchange format of hierarchical omics data and the multi-axis and polyphenic ontology

Research Project

Project/Area Number 26240044
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionTohoku University

Principal Investigator

NAKAYA Jun  東北大学, 医学系研究科, 大学院非常勤講師 (90420463)

Co-Investigator(Kenkyū-buntansha) 荻島 創一  東北大学, 東北メディカル・メガバンク機構, 准教授 (40447496)
立川 察理  東北大学, 医学(系)研究科(研究院), 助手 (90621483)
今井 健  東京大学, 医学(系)研究科(研究院), 講師 (90401075)
永家 聖  東北大学, 東北メディカル・メガバンク機構, 助手 (00726466)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥43,810,000 (Direct Cost: ¥33,700,000、Indirect Cost: ¥10,110,000)
Fiscal Year 2016: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
Fiscal Year 2015: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
Fiscal Year 2014: ¥27,430,000 (Direct Cost: ¥21,100,000、Indirect Cost: ¥6,330,000)
Keywordsオミックス / ICD / 臨床情報モデル / 全ゲノムシーケンス / マークアップ言語 / マルチエントリーポイント / 国際標準化 / 医療情報学 / 生体生命情報学 / データ交換形式 / オントロジー
Outline of Final Research Achievements

In this study, we formulated data exchange format of omics medical data including hierarchical omics data and clinical data. We developed novel data exchange format of multidimensional, multifactorial, multi layered data of hierarchical omics data (from genome to phenome), clinical data, and environmental data, which are separately described by data elements and semantics relationships. We are working on international standardization of our data exchange formats.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (26 results)

All 2017 2016 2015 2014

All Journal Article (16 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 16 results,  Open Access: 9 results,  Acknowledgement Compliant: 5 results) Presentation (9 results) (of which Int'l Joint Research: 6 results,  Invited: 3 results) Book (1 results)

  • [Journal Article] The Human Phenotype Ontology in 2017.2017

    • Author(s)
      Kohler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Ayme S, Baynam G, Bello SM, ... Ogishima S, ...Haendel M.
    • Journal Title

      Nucleic Acids Res

      Volume: 45(D1) Issue: D1 Pages: D865-D876

    • DOI

      10.1093/nar/gkw1039

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Tohoku Medical Megabank Project: Design and Mission2016

    • Author(s)
      Kuriyama S, Yaegashi N, et al. (Tamiya G; 11th in 58 authors)
    • Journal Title

      Journal of Epidemiology

      Volume: 26 Issue: 9 Pages: 493-511

    • DOI

      10.2188/jea.JE20150268

    • NAID

      130005409018

    • ISSN
      0917-5040, 1349-9092
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The structural origin of metabolic quantitative diversity2016

    • Author(s)
      Koshiba S, Motoike I, Kojima K, Hasegawa T, Shirota M, Saito T, Saigusa D, Danjoh I, Katsuoka F, Ogishima S, ... Yamamoto M.
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 31463-31463

    • DOI

      10.1038/srep31463

    • URL

      https://pure.teikyo.jp/en/publications/f23f66dd-859e-4088-8e53-de40d99cc561

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia.2016

    • Author(s)
      Mizuno S, Ogishima S, Nishigori H, Jamieson DG, Verspoor K, Tanaka H, Yaegashi N, Nakaya J.
    • Journal Title

      PLoS One

      Volume: 11(10) Issue: 10 Pages: e0162828-e0162828

    • DOI

      10.1371/journal.pone.0162828

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer's Disease Pathogenesis.2016

    • Author(s)
      Ogishima S, Mizuno S, Kikuchi M, Miyashita A, Kuwano R, Tanaka H, Nakaya J.
    • Journal Title

      Methods Mol Biol.

      Volume: 1303 Pages: 423-32

    • DOI

      10.1007/978-1-4939-2627-5_25

    • ISBN
      9781493926268, 9781493926275
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Network-Based Analysis for Uncovering Mechanisms Underlying Alzheimer's Disease.2016

    • Author(s)
      Kikuchi M, Ogishima S, Mizuno S, Miyashita A, Kuwano R, Nakaya J, Tanaka H.
    • Journal Title

      Methods Mol Biol.

      Volume: 1303 Pages: 479-91

    • DOI

      10.1007/978-1-4939-2627-5_29

    • ISBN
      9781493926268, 9781493926275
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Network Analysis of a Comprehensive Knowledge Repository Reveals a Dual Role for Ceramide in Alzheimer's Disease.2016

    • Author(s)
      Mizuno S, Ogishima S, Kitatani K, Kikuchi M, Tanaka H, Yaegashi N, Nakaya J.
    • Journal Title

      PLoS One.

      Volume: 11 Issue: 2 Pages: e0148431-e0148431

    • DOI

      10.1371/journal.pone.0148431

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Network biology approach to epithelial-mesenchymal transition in cancer metastasis: three stage theory.2015

    • Author(s)
      Tanaka H, Ogishima S.
    • Journal Title

      J Mol Cell Biol

      Volume: 7 Issue: 3 Pages: 253-66

    • DOI

      10.1093/jmcb/mjv035

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals2015

    • Author(s)
      Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Engel J D, Kinoshita K, Kure S, Yaegashi N, Yamamoto M.
    • Journal Title

      Nature Communications

      Volume: 6 Issue: 1 Pages: 8018-8018

    • DOI

      10.1038/ncomms9018

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage.2015

    • Author(s)
      Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO; FANTOM consortium, Okada-Hatakeyama M, Mar JC.
    • Journal Title

      PLoS One.

      Volume: 10(12) Issue: 12 Pages: e0144176-e0144176

    • DOI

      10.1371/journal.pone.0144176

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.2015

    • Author(s)
      Hurst LD, Ghanbarian AT, Forrest AR; FANTOM consortium, Huminiecki L.
    • Journal Title

      PLoS Biol.

      Volume: 13(12) Issue: 12 Pages: e1002315-e1002315

    • DOI

      10.1371/journal.pbio.1002315

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Future Direction of IMIA Standardization. Report from the IMIA Standardization Working Group2014

    • Author(s)
      Nakaya J, Kimura M, Ogishima S, Shabo A, Kim IK, Parisot C, de Faria Leao B
    • Journal Title

      Yearb Med Inform.

      Volume: 9 Issue: 01 Pages: 105-9

    • DOI

      10.15265/iy-2014-0010

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Survey Aimed at General Citizens of the US and Japan about Their Attitudes toward ElectronicMedical Data Handling2014

    • Author(s)
      Michio Kimura , Jun Nakaya , Hiroshi Watanabe , Toshiro Shimizu, Kazuyuki Nakayasu.
    • Journal Title

      International Journal of Environmental Research and Public Health

      Volume: 11 Issue: 5 Pages: 4572-4588

    • DOI

      10.3390/ijerph110504572

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 医学情報学分野の視点から見た未来型医療と東北メディカル・メガバンク事業2014

    • Author(s)
      中谷純
    • Journal Title

      日本歯科医師会雑誌

      Volume: 66

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Clinical Omics sub information model for ICD11(iCOs)2014

    • Author(s)
      Jun Nakaya, Takeshi Imai, Michiyo Kamata, Kaei Hiroi, Hiroshi Tanaka.
    • Journal Title

      WHO-FAMILY OF INTERNATIONAL CLASSIFICATIONS NETWORK ANNUAL MEETING

      Volume: NA

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Clinical Omics sub information model for ICD11(iCOs)2014

    • Author(s)
      Jun Nakaya, Takeshi Imai, Michiyo Kamata, Kaei Hiroi, Hiroshi Tanaka
    • Journal Title

      WHO-FAMILY OF INTERNATIONAL CLASSIFICATIONS NETWORK ANNUAL MEETING

      Volume: NA

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Presentation] 未来型の個別化予防の実現に向けて - 統合・知識データベースの構築2016

    • Author(s)
      荻島創一
    • Organizer
      関西経済連合会 ビッグデータ利活用促進に向けた講演会
    • Place of Presentation
      中之島センタービル(大阪市)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 東北メディカル・メガバンク計画の取り組み - 大規模ゲノムコホートの統合データベース2016

    • Author(s)
      荻島創一
    • Organizer
      専門実務セミナー「個別化医療の現状とこれからの展望・課題 Part2
    • Place of Presentation
      千里ライフサイエンスセンター(豊中市)
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Deep phenotyping toward precision medicine2016

    • Author(s)
      Ogishima S, Tanaka H
    • Organizer
      International Symposium on BioComplexity 2016
    • Place of Presentation
      ビーコンプラザ別府(別府市)
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Panel : Interoperability; Meaningful Exchange of Information from Clinical Omics point of view2015

    • Author(s)
      Jun Nakaya
    • Organizer
      WHO-FAMILY OF INTERNATIONAL CLASSIFICATIONS NETWORK ANNUAL MEETING Plenary
    • Place of Presentation
      Manchester (UK)
    • Year and Date
      2015-10-17
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Progress around Clinical Omics sub information model for ICD (iCOs)2015

    • Author(s)
      Jun Nakaya, Takeshi Imai, Kaei Hiroi, Mika Watari, Hiroshi Tanaka
    • Organizer
      WHO-FAMILY OF INTERNATIONAL CLASSIFICATIONS NETWORK ANNUAL MEETING
    • Place of Presentation
      Manchester (UK)
    • Year and Date
      2015-10-17
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 招待講演「未来型医療、地域医療連携における医療介護福祉情報の変化」2015

    • Author(s)
      中谷純
    • Organizer
      第41回日本診療情報管理学会学術大会
    • Place of Presentation
      岡山コンベンションセンター(岡山)
    • Year and Date
      2015-09-17
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 大会長講演「羅針盤:医療情報学の位置」2015

    • Author(s)
      中谷純
    • Organizer
      第19回医療情報学会春季学術大会
    • Place of Presentation
      仙台国際センター(仙台)
    • Year and Date
      2015-06-12
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Clinical Omics sub information model for ICD11(iCOs)2014

    • Author(s)
      Jun Nakaya, Takeshi Imai, Michiyo Kamata, Kaei Hiroi, Hiroshi Tanaka
    • Organizer
      WHO-FAMILY OF INTERNATIONAL CLASSIFICATIONS NETWORK ANNUAL MEETING
    • Place of Presentation
      Balcelona (Spain)
    • Year and Date
      2014-10-11
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 病院情報システムにおける薬剤禁忌情報の取扱い2014

    • Author(s)
      井上隆輔, 中山雅晴, 中谷純
    • Organizer
      第18回医療情報学会春季学術大会
    • Place of Presentation
      岡山コンベンションセンター(岡山)
    • Year and Date
      2014-06-06
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Book] 改正個人情報保護法でゲノム研究はどう変わるか?-個人識別符号・要配慮情報としてのゲノムデータ2017

    • Author(s)
      清水佳奈, 山本奈津子, 川嶋実苗, 片山俊明, 荻島創一
    • Publisher
      羊土社
    • Related Report
      2016 Annual Research Report

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Published: 2014-04-04   Modified: 2018-03-22  

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