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

• Project/Area Number: 26240044
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Tohoku 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: ¥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.

Research Products

• [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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The Tohoku Medical Megabank Project: Design and Mission (2016)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] The structural origin of metabolic quantitative diversity. (2016)
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Rare variant discovery by deep whole-genome sequencing of 1070 Japanese Individuals (2015)
  • 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
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Future Direction of IMIA Standardization. Report from the IMIA Standardization Working Group (2014)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] A Survey Aimed at General Citizens of the US and Japan about Their Attitudes toward ElectronicMedical Data Handling (2014)
  • 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
  • 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
  • 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
  • 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
  • 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）
  • 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）
  • Invited
• [Presentation] Deep phenotyping toward precision medicine (2016)
  • 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）
  • Invited
• [Presentation] Panel : Interoperability; Meaningful Exchange of Information from Clinical Omics point of view (2015)
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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