Development of ontological representation for disease and cohort information

• Project/Area Number: 15K00295
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Intelligent informatics
• Research Institution: Tohoku University
• Principal Investigator: Takai Takako 東北大学, 東北メディカル・メガバンク機構, 非常勤講師 (60222840)
• Project Period (FY): 2015-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: オントロジー / ゲノムコホート / 個別化予防 / ロール概念 / ゲノムコホート研究 / 法造 / バイオバンク / 東北メディカル・メガバンク事業 / PTSD / 緑内障 / 歯周炎

Outline of Final Research Achievements

An ontology was developed to provide explicit definitions of biomedical concepts obtained in the research on the personalized genome medicine. The concepts of processes and causal relationships are mostly investigated in this study. An ontology based on the axiom theory was firstly constructed in an application of Basic Formal Ontology. Another ontology based on the rule-concept theory was developed in order to specify the roles of individual concepts in their causal relationships to the disease onset and progression. The role-concept theory has an advantage in computation of causal mechanisms among biomedical concepts observed in genome based cohort studies.

Academic Significance and Societal Importance of the Research Achievements

オントロジーは、人間が共有する背景知識を計算機で利用できるよう、演算処理を可能としたものである。個人のゲノム配列情報を利用して個々人の生得の体質に基づく医療の提供を目指すゲノム医療の実現には、疾患、症状、検査、医薬品、生活習慣、栄養、社会活動、等の人間生活を取り巻く様々なデータを解釈するための背景知識を計算機で利用可能とするオントロジーの開発が必要とされている。

Research Products

• [Journal Article] Outlier detection for questionnaire data in biobanks (2019)
  • Author(s): Sakurai Rieko、Ueki Masao、Makino Satoshi、Hozawa Atsushi、Kuriyama Shinichi、Takai-Igarashi Takako、Kinoshita Kengo、Yamamoto Masayuki、Tamiya Gen
  • Journal Title: International Journal of Epidemiology Volume: 印刷中 Issue: 4 Pages: 1305-1315
  • DOI: 10.1093/ije/dyz012
  • Peer Reviewed
• [Journal Article] Respiratory resistance among adults in a population-based cohort study in Northern Japan. (2019)
  • Author(s): Miura E, Tsuchiya N, Igarashi Y, Arakawa R, Nikkuni E, Tamai T, Tabata M, Ohkouchi S, Irokawa T, Ogawa H, Takai-Igarashi T, Suzuki Y, Kuriyama S, Tamiya G, Hozawa A, Yamamoto M, Kurosawa H.
  • Journal Title: Respiratory Investigation Volume: 印刷中 Issue: 3 Pages: 30226-0
  • DOI: 10.1016/j.resinv.2018.12.008
  • Peer Reviewed
• [Journal Article] Maternity Log study: a longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy (2019)
  • Author(s): Sugawara J, Ochi D, Yamashita R, Yamauchi T, Saigusa D, Wagata M, Obara T, Ishikuro M, Tsunemoto Y, 18名略, Hiyama S, Nagasaki M
  • Journal Title: BMJ Open Volume: 9(2) Issue: 2 Pages: e025939-e025939
  • DOI: 10.1136/bmjopen-2018-025939
  • Peer Reviewed / Open Access
• [Journal Article] Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare (2018)
  • Author(s): Yasuda Jun、Kinoshita Kengo、et al.,
  • Journal Title: The Journal of Biochemistry Volume: 165 Issue: 2 Pages: 139-158
  • DOI: 10.1093/jb/mvy096
  • NAID: 40021809939
  • Peer Reviewed / Open Access
• [Journal Article] Genome-wide association study identifies gastric cancer susceptibility loci at 12q24.11-12 and 20q11.21 (2018)
  • Author(s): Tanikawa C, Kamatani Y, Toyoshima O, Sakamoto H, Ito H, Takahashi A, et al.
  • Journal Title: Cancer Science Volume: 109 Issue: 12 Pages: 4015-4024
  • DOI: 10.1111/cas.13815
  • Peer Reviewed / Open Access
• [Journal Article] Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. (2018)
  • Author(s): Koshiba, S., （途中略）, Yamamoto, M.（合計２１名、本研究者は１番目）
  • Journal Title: Genes Cells Volume: 23 Issue: 6 Pages: 406-417
  • DOI: 10.1111/gtc.12588
  • Peer Reviewed / Open Access
• [Journal Article] Epigenetic modulation of Fgf21 in the perinatal mouse liver ameliorates diet-induced obesity in adulthood (2018)
  • Author(s): X Yuan, K Tsujimoto, K Hashimoto, K Kawahori, N Hanzawa, M Hamaguchi, T Seki, M Nawa, T Ehara, Y Kitamura, I Hatada, M Konishi, N Itoh, Y Nakagawa, H Shimano, T Takai-Igarashi, Y Kamei, Y Ogawa.
  • Journal Title: Nature Communications Volume: 9 Issue: 1 Pages: 636-636
  • DOI: 10.1038/s41467-018-03038-w
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2,049 individuals (2018)
  • Author(s): Y Yamaguchi-Kabata, J Yasuda, O Tanabe, Y Suzuki, H Kawame, N Fuse, M Nagasaki, Y Kawai, K Kojima, F Katsuoka, S Saito, I Danjoh, I Motoike, R Yamashita, S Koshiba, D Saigusa, G Tamiya, S Kure, N Yaegashi, Y Kawaguchi, F Nagami, S Kuriyama, J Sugawara, N Minegishi, A Hozawa, T Takai-Igarashi, K Kinoshita, M Yamamoto.
  • Journal Title: Journal of Human Genetics. Volume: 63 Issue: 2 Pages: 213-230
  • DOI: 10.1038/s10038-017-0347-1
  • Peer Reviewed / Open Access
• [Journal Article] Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design (2017)
  • Author(s): Takai-Igarashi T, Kinoshita K, Nagasaki M, Ogishima S, Nakamura N, Nagase S, Nagaie S, Saito T, Nagami F, Minegishi N, Suzuki Y, Suzuki K, Hashizume H, Kuriyama S, Hozawa A, Yaegashi N, Kure S, Tamiya G, Kawaguchi Y, Tanaka H, Yamamoto M
  • Journal Title: BMC Med Inform Decis Mak Volume: 17 Issue: 1 Pages: 100-100
  • DOI: 10.1186/s12911-017-0494-5
  • Peer Reviewed / Open Access
• [Journal Article] 個別化医療・個別化予防を推進するオントロジー (2017)
  • Author(s): 高井貴子
  • Journal Title: CICSJ Bulletin Volume: 35 Pages: 174-179
  • Peer Reviewed
• [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 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] Structural classification of steroid-binding sites on proteins by coarse-grained atomic environment and its correlation with their biological function. (2015)
  • Author(s): Hori-Tanaka Y, Yura K*, Takai-Igarashi T, Tanaka H.
  • Journal Title: Steroids. Volume: 96 Pages: 81-88
  • DOI: 10.1016/j.steroids.2015.01.015
  • Peer Reviewed
• [Journal Article] Identification of Collaborative Activities with Oxidative Phosphorylation in Bipolar Disorder. (2015)
  • Author(s): Sawai H, Takai-Igarashi T*, Tanaka H
  • Journal Title: Bioinformation Volume: １１ Issue: 4 Pages: 207-216
  • DOI: 10.6026/97320630011207
  • Peer Reviewed / Open Access
• [Journal Article] Development of an Ontology for Periodontitis. (2015)
  • Author(s): Suzuki A, Takai-Igarashi T*, Nakaya J, Tanaka H.
  • Journal Title: Journal of Biomedical Semantics Volume: 6 Issue: 1 Pages: 30-30
  • DOI: 10.1186/s13326-015-0028-y
  • Peer Reviewed / Open Access
• [Presentation] Genome Medical Projects in Japan (2019)
  • Author(s): 高井 貴子
  • Organizer: 生物試料の保管及び活用に関する検討会
  • Invited
• [Presentation] Ontology in Bio-medicine (2018)
  • Author(s): 高井 貴子
  • Organizer: バイオにおけるビッグデータ
  • Invited
• [Presentation] ゲノム医療研究プロジェクト (2018)
  • Author(s): 高井 貴子
  • Organizer: データ関連人材プログラム
  • Invited
• [Presentation] ゲノム医療研究を推進するオントロジー研究 (2018)
  • Author(s): 高井 貴子
  • Organizer: 医療情報分析の実際
  • Invited
• [Presentation] GEM-J Project (2018)
  • Author(s): 高井 貴子
  • Organizer: Bio-Hackathon2018
  • Int'l Joint Research / Invited
• [Presentation] Tohoku Medical Megabank Project: a project for personalized preventive medicine based on a biobank and prospective genome cohort studies (2018)
  • Author(s): T Takai-Igarashi.
  • Organizer: Workshop on Bioinformatics of Gene Regulation
  • Int'l Joint Research / Invited
• [Presentation] 個別化医療・個別化予防を推進するオントロジー (2017)
  • Author(s): 高井貴子
  • Organizer: 第380回CBI学会研究講演会
  • Place of Presentation: 大阪, ナレッジキャピタル北館タワー
  • Year and Date: 2017-02-03
• [Presentation] Security Controls in an Integrated Biobank to Protect Privacy in Data Sharing (2017)
  • Author(s): T Takai-Igarashi, K Kinoshita, M Nagasaki, S Ogishima, N Nakamura, S Nagase, S Nagaie, T Saito, F Nagami, N Minegishi, Y Suzuki, K Suzuki, H Hashizume, S Kuriyama, A Hozawa, N Yaegashi, S Kure, G Tamiya, Y Kawaguchi, H Tanaka, and M Yamamoto
  • Organizer: International Workshop on Artificial Life and Robotics
  • Int'l Joint Research
• [Presentation] Residential place and oral health after the great east Japan earthquake (2017)
  • Author(s): S Koyama, J Aida, T Takai-Igarashi, A Hozawa, A Otsuki, J Kawashima, H Matsui, A Tsuboi, K Osaka, M Yamamoto.
  • Organizer: The 65th Annual Meeting of Japanese Association for Dental Research
  • Int'l Joint Research
• [Presentation] Maternal Oral Microbiota Profile Associated with Hypertensive Disorders of Pregnancy (2017)
  • Author(s): T Yamauchi, D Ochi, R Yamashita, M Wagata, J Kawashima, Y Tsunemoto, Y Harada, T Takai-Igarashi, O Tanabe, S Hiyama, M Nagasaki, J Sugawara
  • Organizer: American Society of Human Genetics (ASHG) Annual Meeting.
  • Int'l Joint Research
• [Presentation] Aim and Progress of Tohoku Medical Megabank Project (2017)
  • Author(s): T Takai-Igarashi
  • Organizer: Environmental Hazards in Multigenerational Disease -Epigenetic Mechanismscs Strategic Planning Conference
  • Int'l Joint Research / Invited
• [Presentation] 前向きコホート、医療情報、個人の疾患感受性多型情報を統合するオントロジーの開発 (2016)
  • Author(s): 高井貴子
  • Organizer: 2016年度人工知能学会全国大会 (第30回)
  • Place of Presentation: 北九州, 北九州国際会議場
  • Year and Date: 2016-06-07
• [Presentation] 前向きコホート、医療情報、個人の疾患感受性多型情報を統合するオントロジーの開発 (2016)
  • Author(s): 高井 貴子
  • Organizer: 2016年度 人工知能学会全国大会（第30回）
  • Place of Presentation: 北九州国際会議場（福岡県北九州市）
  • Year and Date: 2016-06-06
• [Presentation] 医療オントロジーの現状と展望」にて「ゲノム領域におけるオントロジー開発 (2016)
  • Author(s): 高井貴子
  • Organizer: 第20回日本医療情報学会春季学術大会（2016年度）
  • Place of Presentation: 島根, くにびきメッセ
  • Year and Date: 2016-06-04
• [Book] 人工知能学大事典 (2017)
  • Author(s): 高井貴子
  • Total Pages: 1579
  • Publisher: 共立出版
  • ISBN: 4320124200
• [Book] 疾患データベースとバイオバンク (2017)
  • Author(s): 高井貴子
  • Total Pages: 229
  • Publisher: 羊土社
  • ISBN: 4758103666