Yuki Yamagata

Joined

May 2025

Names

Yuki Yamagata (Preferred)

Emails

****@riken.jp (Confirmed)

Personal Links

Career & Education History

Researcher

R-IH, RIKEN (riken.jp)

2023 – 2025

Researcher

BioResource Research Center, RIKEN (riken.jp)

2023 – 2025

Researcher

BDR, RIKEN (riken.jp)

2020 – 2023

Advisors, Relations & Conflicts

No relations added

Expertise

Ontology

2015 – 2025

Publications

SSBD Ontology: A Two-Tier Approach for Interoperable Bioimaging Metadata
Yuki Yamagata, Koji Kyoda, Hiroya Itoga, Emi Fujisawa, Shuichi Onami
- CoRR 2025
- Readers: Everyone
MA-COIR: Leveraging Semantic Search Index and Generative Models for Ontology-Driven Biomedical Concept Recognition
Shanshan Liu, Noriki Nishida, Rumana Ferdous Munne, Narumi Tokunaga, Yuki Yamagata, Kouji Kozaki, Yuji Matsumoto
- CoRR 2025
- Readers: Everyone
Zero-Shot Entailment Learning for Ontology-Based Biomedical Annotation Without Explicit Mentions
Rumana Ferdous Munne, Noriki Nishida, Shanshan Liu, Narumi Tokunaga, Yuki Yamagata, Kouji Kozaki, Yuji Matsumoto
- COLING 2025
- Readers: Everyone
Homeostasis imbalance process ontology: a study on COVID-19 infectious processes
Yuki Yamagata, Tatsuya Kushida, Shuichi Onami, Hiroshi Masuya
- BMC Medical Informatics Decis. Mak. 2024
- Readers: Everyone
Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles
Oumaima El Khettari, Noriki Nishida, Shanshan Liu, Rumana Ferdous Munne, Yuki Yamagata, Solen Quiniou, Samuel Chaffron, Yuji Matsumoto
- BioNLP@ACL 2024
- Readers: Everyone
Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology
Yuki Yamagata, Shuichi Onami, Hiroshi Masuya
- ICBO 2022
- Readers: Everyone
Ontology Integration for Discovering Bioresources Contributing to Medical Science Research
Tatsuya Kushida, Daiki Usuda, Toyoyuki Takada, Yuki Yamagata, Hiroshi Masuya
- ICBO 2022
- Readers: Everyone
A Community Effort for COVID-19 Ontology Harmonization
Asiyah Yu Lin, Yuki Yamagata, William D. Duncan, Leigh C. Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He
- ICBO 2021
- Readers: Everyone
TXPO: A Toxic Process Ontology for Better Understanding of Drug-Induced Liver Injury
Yuki Yamagata, Yoshinobu Igarashi, Noriyuki Nakatsu, Hiroshi Yamada
- ICBO 2019
- Readers: Everyone
Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
- J. Biomed. Semant. 2017
- Readers: Everyone

View all 18 publications

Co-Authors

View all 34 co-authors