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Expansion of the informational technologies for mutual use of measurement data in biological science

Research Project

Project/Area Number 15H02755
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Intelligent informatics
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

MASUYA Hiroshi  国立研究開発法人理化学研究所, バイオリソースセンター, ユニットリーダー (40321814)

Co-Investigator(Kenkyū-buntansha) 古崎 晃司  大阪大学, 産業科学研究所, 准教授 (00362624)
溝口 理一郎  北陸先端科学技術大学院大学, サービスサイエンス研究センター, 特任教授 (20116106)
Co-Investigator(Renkei-kenkyūsha) ONAMI Shuichi  国立研究開発法人理化学研究所, 生命システム研究センター, チームリーダー (50348843)
MASHIMO Tomoji  大阪大学, 大学院医学系研究科附属動物実験施設, 准教授 (80397554)
TAKADA Toyoyuki  国立遺伝学研究所, 哺乳動物遺伝研究室, 助教 (20356257)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000)
Fiscal Year 2017: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2016: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2015: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Keywords情報統合 / オントロジー / 相互利用 / 分野横断 / オープンデータ / 大規模データ / 視点転換 / ロール概念 / 表現型 / 計測データ / 知識の相互利用 / 生命科学データ / 科学データ / 生命科学 / 知識モデル / 知識抽出
Outline of Final Research Achievements

We developed a software tool to supprt editing of large-sized data with highly structured data schema representing context dependency of ontology concepts. The software tool provides functions of bulk editing of Hozo-formatted ontology data with spreadsheet program like operation. This tool is also useful for ontology refinement to improve consistency of data structure from upper classes to instances. As the recent progress of open data activity, improvement of data access methodologies to extremely large-sized and variety of open data becomes expected. This study provide a methodology of the efficient construction of large-sized data with complicated structure such as context dependency and viewpoint conversion, which may contribute to improve utility of open data across domains.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (60 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (7 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 7 results,  Open Access: 7 results) Presentation (46 results) (of which Int'l Joint Research: 16 results,  Invited: 9 results) Book (2 results) Remarks (1 results)

  • [Int'l Joint Research] European Bioinformatics Institute/Medical Research Council/Wellcome Trust Sanger Institute(英国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Jackson Laboratory/University of California/Baylor College of Medicine(米国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Helmholtz Zentrum München(ドイツ)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Institut Clinique de la Souris(フランス)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Identification of genetic elements in metabolism by high-throughput mouse phenotyping2018

    • Author(s)
      Rozman J. et al.
    • Journal Title

      Nat Commun.

      Volume: 9 Issue: 1 Pages: 288-288

    • DOI

      10.1038/s41467-017-01995-2

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction2017

    • Author(s)
      Bowl Michael R.et al.
    • Journal Title

      Nat Commun

      Volume: 8 Issue: 1 Pages: 886-886

    • DOI

      10.1038/s41467-017-00595-4

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Prevalence of sexual dimorphism in mammalian phenotypic traits2017

    • Author(s)
      Karp Natasha A. et al.
    • Journal Title

      Nat Commun.

      Volume: 8 Issue: 1 Pages: 15475-15475

    • DOI

      10.1038/ncomms15475

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences2016

    • Author(s)
      Kobayashi Norio、Lenz Kai、Masuya Hiroshi
    • Journal Title

      Semantic Technology:JIST2016

      Volume: 10055 Pages: 99-115

    • DOI

      10.1007/978-3-319-50112-3_8

    • ISBN
      9783319501116, 9783319501123
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Semantic Data Acquisition by Traversing Class?Class Relationships Over Linked Open Data2016

    • Author(s)
      Yamaguchi Atsuko、Kozaki Kouji、Lenz Kai、Yamamoto Yasunori、Masuya Hiroshi、Kobayashi Norio
    • Journal Title

      Semantic Technology:JIST2016

      Volume: 10055 Pages: 136-151

    • DOI

      10.1007/978-3-319-50112-3_11

    • ISBN
      9783319501116, 9783319501123
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Principles and application of LIMS in mouse clinics2015

    • Author(s)
      Maier H 他29名
    • Journal Title

      Mammalian Genome

      Volume: 26 Issue: 9-10 Pages: 467-481

    • DOI

      10.1007/s00335-015-9586-7

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Applying the ARRIVE Guidelines to an In Vivo Database.2015

    • Author(s)
      Karp NA 他29名
    • Journal Title

      PLoS Biology

      Volume: 13 Issue: 5 Pages: e1002151-e1002151

    • DOI

      10.1371/journal.pbio.1002151

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 実験動物の表現型と疾患との関連性を示すデータベース2017

    • Author(s)
      桝屋啓志、 高月照江、 谷川紀子、 高山英紀、 佐藤道比古、 田中信彦
    • Organizer
      第64回日本実験動物学会総会
    • Related Report
      2017 Annual Research Report
  • [Presentation] モデル生物表現型データポータルサイト J-phenome における情報統合の現状2017

    • Author(s)
      高月照江、 高山英紀、 佐藤道比古、 谷川紀子、 高田豊行、 庫本高志、 成瀬清、 若菜茂晴、 田中信彦、 桝屋啓志
    • Organizer
      第64回日本実験動物学会総会
    • Related Report
      2017 Annual Research Report
  • [Presentation] モデル生物表現型の統合データベース J-Phenome2017

    • Author(s)
      桝屋啓志、 高月照江、 高山英紀、 佐藤道比古、 谷川紀子、 田中信彦
    • Organizer
      第30回モロシヌス研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Morphomics Analysis in Rat Brain Tissues Using Scanning Electron Microscopy and Development of Metadatabase for The Microstructure Imaging Data /走査型電子顕微鏡を用いたラット脳組織の網羅的微細構造解析、 および脳組織画像メタデータベースの構築2017

    • Author(s)
      Kume S、 Maeda M、 Eguchi A、 Kobayashi N、 Masuya H、 Yamato M、 Tamura Y、 Takata K、 Suga M、 Kataoka Y
    • Organizer
      第40回日本神経科学大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Integration of mouse phenotype data2017

    • Author(s)
      Masuya H
    • Organizer
      2017 AMMRA & AMPC Meeting
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RDF-based integration of phenotype data of experimental animals in Japan2017

    • Author(s)
      Masuya H
    • Organizer
      NIX-odML Global Workshop & Hackathon 2017 in Japan
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] モデル生物表現型の統合データベース J-Phenome2017

    • Author(s)
      桝屋啓志、 高月照江、 高山英紀、 佐藤道比古、 谷川紀子、 野村麻美、 田中信彦、 小林紀郎
    • Organizer
      トーゴーの日シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] LOD上の情報をクラス間関係で切り取る基盤技術開発2017

    • Author(s)
      山口敦子、 小林紀郎、 山本泰智、 桝屋啓志、 古崎晃司
    • Organizer
      トーゴーの日シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 理研メタデータベース:分野を超えたデータ駆動型研究を支えるメタデータ利活用基盤2017

    • Author(s)
      小林紀郎、 久米慧嗣、 桝屋啓志
    • Organizer
      トーゴーの日シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 生命科学系超微細構造画像データを運用する統合メタデータベースの構築2017

    • Author(s)
      久米慧嗣、 桝屋啓志、 片岡洋祐、 小林紀郎
    • Organizer
      トーゴーの日シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 表現型データ統合データベースJ-Phenomeにおける計測メタデータの整理統合2017

    • Author(s)
      桝屋啓志
    • Organizer
      2017年度生命科学系学会合同年次大会(ConBio2017)
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] マウス表現型間の関係性の全景2017

    • Author(s)
      田中信彦、 桝屋啓志
    • Organizer
      2017年度生命科学系学会合同年次大会(ConBio2017)
    • Related Report
      2017 Annual Research Report
  • [Presentation] 国内発表現型情報の統合と利活用向上を目指すJ-Phenomeプロジェクト2017

    • Author(s)
      桝屋啓志
    • Organizer
      第10回NBRPデータベース研究会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] RDF based integration of biological phenotype data produced in Japan2017

    • Author(s)
      Masuya H
    • Organizer
      International Symposium on Designing Semantics
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生物表現型ビッグデータの形成に向けて:セマンティックWeb技術を用いた表現型データの統合2016

    • Author(s)
      桝屋啓志、小林紀郎
    • Organizer
      第2回理化学研究所・産業技術総合研究所 共同シンポジウム
    • Place of Presentation
      産業技術総合研究所(茨城県つくば市)
    • Year and Date
      2016-02-02
    • Related Report
      2015 Annual Research Report
  • [Presentation] Data integration of phenotype data of disease model animals using Resource2016

    • Author(s)
      Masuya H
    • Organizer
      IMPC-INFRAFRONTIER Strasburg meeting
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Data integration of phenotype data of disease model animals using Resource Description Framework2016

    • Author(s)
      Masuya H
    • Organizer
      2016 AMMRA&AMPC Meeting
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] RIKEN MetaDatabase: a life-science database integration and publication platform based on the Semantic Web2016

    • Author(s)
      Kobayashi N、 Yamaguchi Y、 Masuya H
    • Organizer
      4th INCF Japan Node International Workshop and 14th INCF Nodes Workshop
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 実験動物の利用拡大に向けたデータベース構築2016

    • Author(s)
      桝屋啓志、高月照江、斎藤実香子、高山英紀、大島和也、田中信彦、戀津魁、小林紀郎
    • Organizer
      第63回日本実験動物学会総会
    • Related Report
      2016 Annual Research Report
  • [Presentation] 理研BRC 日本マウスクリニック: コミュテーへの貢献とIMPCの進捗2016

    • Author(s)
      小林喜美男、鈴木智広、金田秀貴、田村勝、三浦 郁生、古瀬民生、山田郁子、綾部信哉、吉木淳、田中信彦、桝屋啓志、小幡裕一、若菜茂晴
    • Organizer
      第63回日本実験動物学会総会
    • Related Report
      2016 Annual Research Report
  • [Presentation] 実験動物の利用拡大に向けたデータベース構築2016

    • Author(s)
      高月照江、斎藤実香子、高田豊行、庫本高志、成瀬清、若菜茂晴、田中信彦、桝屋啓志
    • Organizer
      第63回日本実験動物学会総会
    • Related Report
      2016 Annual Research Report
  • [Presentation] 新規Col2a1変異マウスを用いたトーランス型扁平椎異形成症の病態機序の検討2016

    • Author(s)
      木村允、市村鋭、桝屋啓志、鈴木智広、若菜茂晴、古市達哉
    • Organizer
      第63回日本実験動物学会総会
    • Related Report
      2016 Annual Research Report
  • [Presentation] RDF技術を用いた疾患モデル動物の表現型データの統合と利用拡大2016

    • Author(s)
      桝屋啓志、高月照江、斎藤実香子、高山英紀、大島和也、田中信彦、戀津魁、小林紀郎
    • Organizer
      2016年度 人工知能学会全国大会
    • Related Report
      2016 Annual Research Report
  • [Presentation] J-phenome: a portal of Japanese phenotype data2016

    • Author(s)
      Masuya H
    • Organizer
      BioHackathon 2016 Symposium
    • Related Report
      2016 Annual Research Report
  • [Presentation] 表現型データ共有のためのデータベースポータル:J-phenome2016

    • Author(s)
      桝屋啓志、高月照江、斎藤実香子、高山英紀、大島和也、田中信彦
    • Organizer
      日本遺伝学会第88回大会
    • Related Report
      2016 Annual Research Report
  • [Presentation] A portal of biological phenotype data of experimental animals produced in Japan2016

    • Author(s)
      Masuya H
    • Organizer
      The 8th ANRRC International Meeting
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生物表現型のRDFデータ作成とそのメリット2016

    • Author(s)
      桝屋啓志
    • Organizer
      第5回生命医薬情報学連合大会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 理研メタデータベースの運用とデータ統合の実際2016

    • Author(s)
      戀津魁、桝屋啓志、小林紀郎
    • Organizer
      トーゴーの日シンポジウム2016
    • Related Report
      2016 Annual Research Report
  • [Presentation] 信頼性が確保されたSPARQLエンドポイントでのクエリ生成支援2016

    • Author(s)
      山口敦子、山本泰智、古崎晃司、戀津魁、桝屋啓志、小林紀郎
    • Organizer
      トーゴーの日シンポジウム2016
    • Related Report
      2016 Annual Research Report
  • [Presentation] RDFを利用して実験動物の表現型と疾患との関連性を示すシステム2016

    • Author(s)
      熊谷禎洋、高月照江、斎藤実香子、高山英紀、桝屋啓志
    • Organizer
      トーゴーの日シンポジウム2016
    • Related Report
      2016 Annual Research Report
  • [Presentation] 生物種横断的な表現型データポータルサイトJ-phenomeについて2016

    • Author(s)
      高月照江、斎藤実香子、高山英紀、大島和也、田中信彦、熊谷禎洋、桝屋啓志
    • Organizer
      トーゴーの日シンポジウム2016
    • Related Report
      2016 Annual Research Report
  • [Presentation] 生物の表現型が研究コミュニティをつなぐ2016

    • Author(s)
      桝屋啓志
    • Organizer
      トーゴーの日シンポジウム2016
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] RIKEN MetaDatabase: a database publication platform for RIKENs life-science researchers that promotes research collaborations over different research area2016

    • Author(s)
      Lenz K、 Masuya H、 Kobayashi N
    • Organizer
      The 15th International Semantic Web Conference (ISWC2016)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of an ontology for an integrated image analysis platform to enable global sharing of microscopy imaging data2016

    • Author(s)
      Kume S、 Masuya H、 Kataoka Y、 Kobayashi N
    • Organizer
      The 15th International Semantic Web Conference (ISWC2016)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Data acquisition by traversing Class-Class relationships over the linked open data2016

    • Author(s)
      Yamaguchi A、 Kozaki K、 Lenz K、 Yamamoto Y、 Masuya H、 Kobayashi N
    • Organizer
      The 15th International Semantic Web Conference (ISWC2016)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A RDF-Based portal of biological phenotype data created in Japan2016

    • Author(s)
      Takatsuki T、 Saito M、 Kumagai S、 Takayama E、 Ohshima K、 Ohshiro N、 Lenz K、 Tanaka N、 Kobayashi N、 Masuya H
    • Organizer
      The 15th International Semantic Web Conference (ISWC2016)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RIKEN MetaDatabase: a database platform as a microcosm of linked open data cloud in the life sciences2016

    • Author(s)
      Kobayashi N、 Lenz K and Masuya H
    • Organizer
      Joint International Semantic Technology Conference 2016 (JIST 2016)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Semantic Data Acquisition by Traversing Class-Class Relationships over the Linked Open Data2016

    • Author(s)
      Yamaguchi A、 Kozaki K、 Lenz K、 Yamamoto Y、 Masuya H and Kobayashi N
    • Organizer
      Joint International Semantic Technology Conference 2016 (JIST 2016)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RDF-Based data sharing of phenotype data of experimental animals produced from Japan2016

    • Author(s)
      Masuya H
    • Organizer
      The 4th International Conference on Rare and Undiagnosed Diseases
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生物種横断的な表現型データポータルサイトJ-phenomeについて2016

    • Author(s)
      高月照江、斎藤実香子、髙山英紀、大島和也、田中信彦、熊谷禎洋、桝屋啓志
    • Organizer
      第39回日本分子生物学会年会
    • Related Report
      2016 Annual Research Report
  • [Presentation] 網羅的マウス表現型データのアソシエーション分析による表現形質間の関係性の提示と予測2016

    • Author(s)
      田中信彦、桝屋啓志
    • Organizer
      第39回日本分子生物学会年会
    • Related Report
      2016 Annual Research Report
  • [Presentation] RDF-based data sharing of bio-resource related information2015

    • Author(s)
      Hiroshi Masuya, Terue Takatsuki, Mikako Saito, Eiki Takayama, Kazuya Ohshima, Nozomu Ohshiro, Kai Lenz, Nobuhiko Tanaka, Hiroshi Mori, Shuichi Kawashima and Norio Kobayashi
    • Organizer
      SWAT4LS International Conference
    • Place of Presentation
      Cambridge, United Kingdom
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 表現型情報統合データベースのためのデータ作成2015

    • Author(s)
      高月 照江、齋藤 実香子、大島 和也、高山 英紀、金子 裕代、成瀬 清、若菜 茂晴、田中 信彦、桝屋 啓志
    • Organizer
      第38回分子生物学会年会・第88回生化学会大会合同大会(BMB2015: Biochemistry and Molecular Biology 2015)
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-03
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] セマンティックWeb技術を用いたバイオリソースデータの標準化と整備2015

    • Author(s)
      桝屋啓志
    • Organizer
      第1回理化学研究所・産業技術総合研究所 共同シンポジウム
    • Place of Presentation
      産業技術総合研究所(東京都江東区)
    • Year and Date
      2015-06-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] 生物種を超えた表現型情報統合のためのデータ作成2015

    • Author(s)
      高月照江、矢田有加里、斎藤実香子、高田豊行、真下知士、成瀬清、若菜茂晴、田中信彦、桝屋啓志
    • Organizer
      第62回日本実験動物学会総会
    • Place of Presentation
      京都テルサ(京都府京都市)
    • Year and Date
      2015-06-08
    • Related Report
      2015 Annual Research Report
  • [Presentation] 生物表現型情報と、疾患情報をつなげるデータベース2015

    • Author(s)
      桝屋 啓志、高山 英起、古崎 晃司、今井 健、大江 和彦、溝口 理一郎
    • Organizer
      2015年度人工知能学会全国大会(第29回)
    • Place of Presentation
      公立はこだて未来大学(北海道函館市)
    • Year and Date
      2015-05-30
    • Related Report
      2015 Annual Research Report
  • [Book] 人工知能学大辞典2017

    • Author(s)
      人工知能学会編
    • Total Pages
      1600
    • Publisher
      共立出版
    • ISBN
      9784320124202
    • Related Report
      2017 Annual Research Report
  • [Book] マウス表現型解析スタンダード2016

    • Author(s)
      伊川 正人、若菜 茂晴、高橋 智
    • Total Pages
      347
    • Publisher
      羊土社
    • ISBN
      9784758101981
    • Related Report
      2016 Annual Research Report
  • [Remarks] マウス・ラット表現型・疾患関連データベース

    • URL

      http://phenomodel.riken.jp

    • Related Report
      2015 Annual Research Report

URL: 

Published: 2015-04-16   Modified: 2022-08-26  

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