Yamagata Yuki 山縣友紀

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Yuki Yamagata 山縣友紀

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Researcher Number	00543927
Other IDs	https://orcid.org/0000-0002-9673-1283
Affiliation (Current)	2026: 国立研究開発法人理化学研究所, バイオリソース研究センター, 研究員
Affiliation (based on the past Project Information) *help	2023 – 2024: 国立研究開発法人理化学研究所, 情報統合本部, 研究員 2022: 国立研究開発法人理化学研究所, 生命機能科学研究センター, 研究員
Review Section/Research Field	Principal Investigator Basic Section 61030:Intelligent informatics-related
Keywords	Principal Investigator 感染機序 / リスク低減 / 知識統合 / 知識表現 / COVID-19 / オントロジー

Knowledge integration and application for reducing the risk of COVID-19 severity based on ontologyPrincipal Investigator
- Principal Investigator
  
  Yuki Yamagata
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 61030:Intelligent informatics-related
- Research Institution
  Institute of Physical and Chemical Research

All 2025 2024 2023 2022

All Journal Article Presentation

[Journal Article] Survey on large language model annotation of cellular senescence from figures in review articles2024
- Author(s)
  Yamagata Yuki、Yamada Ryota
- Journal Title
  
  Genomics & Informatics
  
  Volume: 22 Issue: 1
- DOI
  10.1186/s44342-024-00011-6
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K17959
[Journal Article] BioHackJP 2023 Report R1:Improving phenotype ontology interoperability2024
- Author(s)
  Dohi Eisuke、Kushida Tatsuya、Yamagata Yuki、Takatsuki Terue、Shin Jaemoon、Masuya Hiroshi、Liener Thomas、Hoehndorf Robert
- Journal Title
  
  BioHackrXiv
  
  Volume: －
- DOI
  10.37044/osf.io/d27fw
- Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Journal Article] Homeostasis imbalance process ontology: a study on COVID-19 infectious processes2024
- Author(s)
  Yamagata Yuki、Kushida Tatsuya、Onami Shuichi、Masuya Hiroshi
- Journal Title
  
  BMC Medical Informatics and Decision Making
  
  Volume: 23 Issue: S4
- DOI
  10.1186/s12911-024-02516-0
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K17959
[Journal Article] SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data2024
- Author(s)
  Kyoda Koji、Itoga Hiroya、Yamagata Yuki、Fujisawa Emi、Wang Fangfang、Miranda-Miranda Miguel、Yamamoto Haruna、Nakano Yasue、Tohsato Yukako、Onami Shuichi
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 53 Issue: D1 Pages: D1716-D1723
- DOI
  10.1093/nar/gkae860
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22K17959
[Journal Article] Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles2024
- Author(s)
  Oumaima El Khettari, Noriki Nishida, Shanshan Liu, Rumana Ferdous Munne, Yuki Yamagata, Solen Quiniou, Samuel Chaffron, Yuji Matsumoto
- Journal Title
  
  Proceedings of the 23rd Workshop on Biomedical Natural Language Processing
  
  Volume: 1 Pages: 457-473
- DOI
  10.18653/v1/2024.bionlp-1.37
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K17815, KAKENHI-PROJECT-22K17959
[Journal Article] Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective2024
- Author(s)
  Yamagata Yuki、Fukuyama Tsubasa、Onami Shuichi、Masuya Hiroshi
- Journal Title
  
  Scientific Data
  
  Volume: 11 Issue: 1
- DOI
  10.1038/s41597-024-03331-y
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Enhancing Global Knowledge Interoperability for Bioimaging through Ontology Utilization2025
- Author(s)
  Yuki Yamagata, Koji Kyoda, Hiroya Itoga, Emi Fujisawa, Shuichi Onami
- Organizer
  RIKEN Symposia: OLSP Symposium 2025 - Present and Future Perspectives of Open Life Sciences ?
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Metadata and file formats for global sharing of bioimaging data2025
- Author(s)
  Koji Kyoda, Hiroya Itoga, Yuki Yamagata, Emi Fujisawa, Miguel Miranda, Shuichi Onami
- Organizer
  RIKEN Symposia: OLSP Symposium 2025 - Present and Future Perspectives of Open Life Sciences -
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD: Global Sharing of Bioimaging Data - Management and Implementation2025
- Author(s)
  Hiroya Itoga, Koji Kyoda, Yuki Yamagata, Haruna Yamamoto, Miguel Miranda Miranda, Yukako Tohsato, Shuichi Onami
- Organizer
  BDR-NCBS Joint Meeting
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD: Global sharing of bioimaging data2025
- Author(s)
  Hiroya Itoga, Koji Kyoda, Yuki Yamagata, Emi Fujisawa, Haruna Yamamoto, Miguel Miranda Miranda, Yukako Tohsato, Shuichi Onami
- Organizer
  The 5th Kobe University-RIKEN BDR Joint Symposium/第5回神戸大学‐理研BDR合同シンポジウム
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Mapping and gap analysis for metadata harmonization of bioimaging data resources2024
- Author(s)
  Koji Kyoda, Yuki Yamagata, Hiroya Itoga, Shuichi Onami
- Organizer
  Global BioImaging Exchange of Experience 2024
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Metadata and File Formats for Global Sharing of Bioimaging Data2024
- Author(s)
  Koji Kyoda, Hiroya Itoga, Yuki Yamagata, Emi Fujisawa, Miguel Miranda-Miranda, Shuichi Onami
- Organizer
  統合化推進プログラム（DICP）2024年度研究交流会
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD: Global sharing of bioimaging data2024
- Author(s)
  Hiroya Itoga, Emi Fujisawa, Haruna Yamamoto, Miguel Miranda Miranda, Yuki Yamagata, Koji Kyoda, Yukako Tohsato, Shuichi Onami
- Organizer
  Global BioImaging Exchage of Experience 2024
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] グローバルなバイオイメージングデータ共有に向けたメタデータとデータフォーマット2024
- Author(s)
  京田耕司, 糸賀裕弥, 山縣友紀, 藤澤絵美, ミランダミゲル, 大浪修一
- Organizer
  トーゴーの日シンポジウム2024
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Landscape analysis of metadata usage in major bioimage repositories2024
- Author(s)
  Shuichi Onami, Koji Kyoda, Yuki Yamagata
- Organizer
  foundingGIDE Community Event 2024
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Online databases and data integration in the RIKEN BioResource Research Center2024
- Author(s)
  桝屋啓志, 高田豊行, 臼田大輝, 湯原直美, 栗原恵子, 並木由理, 岩瀬秀, 鈴木健大, 山縣友紀, 粕川雄也, 川路英哉, 沖真弥, 櫛田達矢
- Organizer
  The Allied Genetics Conference (TAGC)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] オントロジー開発のための大規模言語モデルを用いた生命医学論文図アノテーションの試み2024
- Author(s)
  山縣友紀, 山田涼太, 大浪修一, 桝屋啓志
- Organizer
  2024年度人工知能学会全国大会（第38回）
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD: バイオイメージングデータのグローバルな共有2024
- Author(s)
  京田耕司, 糸賀裕弥, 山縣友紀, ミランダミゲル, 山本春菜, 藤澤絵美, 遠里由佳子, 大浪修一
- Organizer
  第47回日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] 表現型データの類似度に基づく疾患モデル生物推定2024
- Author(s)
  櫛田達矢, 申在紋, 臼田大輝, 山縣友紀, 高田豊行, 小林紀郎, 藤原豊史, 桝屋啓志
- Organizer
  2024年度人工知能学会全国大会 (第38回)
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] バイオイメージング知識互換と運用性向上のためのオントロジー利活用に向けた取り組み2024
- Author(s)
  山縣友紀, 京田耕司, 糸賀裕弥, 藤澤絵美, 大浪修一
- Organizer
  統合化推進プログラム（DICP）2024年度研究交流会
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] グローバルなバイオイメージングデータ相互運用性実現に向けたオントロジー分析2024
- Author(s)
  山縣友紀, 京田耕司, 糸賀裕弥, 藤澤絵美, 大浪修一
- Organizer
  トーゴーの日シンポジウム2024
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD:repository/SSBD:database: A global sharing of bioimaging data2023
- Author(s)
  2.京田耕司, 糸賀裕弥, Wang Fangfang, 山本春菜, ミランダ-ミランダミゲル, 山縣友紀, 遠里由佳子, 大浪修一:
- Organizer
  The 56th Annual Meeting of the Japanese Society of Developmental Biologist
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD: バイオイメージングデータのグローバルなデータ共有2023
- Author(s)
  京田耕司, 糸賀裕弥, 王放放, 山縣友紀, ミランダ-ミランダミゲル, 山本春菜, 遠里由佳子, 大浪修一:
- Organizer
  第75回日本細胞生物学会大会
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] 老化制御を目指した細胞老化オントロジーモデリング2023
- Author(s)
  山縣友紀, 大浪修一，桝屋啓志
- Organizer
  2023年度人工知能学会全国大会（第37回）
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] SSBD:repository/SSBD:database: A global sharing of bioimaging dat2023
- Author(s)
  3.京田耕司, 糸賀裕弥, Wang Fangfang, 山本春菜, ミランダ-ミランダミゲル, 山縣友紀, 遠里由佳子, 大浪修一
- Organizer
  The 20th International Microscopy Congress
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] オントロジーに基づく細胞老化プロセスの知識記述モデリング2022
- Author(s)
  山縣友紀
- Organizer
  第45回日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-22K17959
[Presentation] Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology2022
- Author(s)
  Yuki Yamagata
- Organizer
  ICBO 2022: International Conference on Biomedical Ontology
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K17959

1. 西田典起

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Yamagata Yuki 山縣 友紀

Yuki Yamagata 山縣 友紀

Research Projects

Research Products

Co-Researchers

Knowledge integration and application for reducing the risk of COVID-19 severity based on ontologyPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Survey on large language model annotation of cellular senescence from figures in review articles2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] BioHackJP 2023 Report R1:Improving phenotype ontology interoperability2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Homeostasis imbalance process ontology: a study on COVID-19 infectious processes2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective2024

Author(s)

Journal Title

DOI

Data Source

[Presentation] Enhancing Global Knowledge Interoperability for Bioimaging through Ontology Utilization2025

Author(s)

Organizer

Data Source

[Presentation] Metadata and file formats for global sharing of bioimaging data2025

Author(s)

Organizer

Data Source

[Presentation] SSBD: Global Sharing of Bioimaging Data - Management and Implementation2025

Author(s)

Organizer

Data Source

[Presentation] SSBD: Global sharing of bioimaging data2025

Author(s)

Organizer

Data Source

[Presentation] Mapping and gap analysis for metadata harmonization of bioimaging data resources2024

Author(s)

Organizer

Data Source

[Presentation] Metadata and File Formats for Global Sharing of Bioimaging Data2024

Author(s)

Organizer

Data Source

[Presentation] SSBD: Global sharing of bioimaging data2024

Author(s)

Organizer

Data Source

[Presentation] グローバルなバイオイメージングデータ共有に向けたメタデータとデータフォーマット2024

Author(s)

Organizer

Data Source

[Presentation] Landscape analysis of metadata usage in major bioimage repositories2024

Author(s)

Organizer

Data Source

[Presentation] Online databases and data integration in the RIKEN BioResource Research Center2024

Author(s)

Organizer

Yamagata Yuki 山縣友紀

Yuki Yamagata 山縣友紀

[Presentation] バイオイメージング知識互換と運用性向上のためのオントロジー利活用に向けた取り組み2024