Event Ontology: A Pathway-Centric Ontology for Biological Processes. - Tatsuya Kushida; Toshihisa Takagi; Ken-ichiro Fukuda (Pacific Symposium on Biocomputing, 2006)

Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis. - Tatsuya Kushida; Takao Asanuma; Yoshihiro Okuda; Yo Shidahara; Toshihisa Takagi (CISIS, 2009)

An Advanced Strategy for Integration of Biological Measurement Data. - Hiroshi Masuya; Georgios V. Gkoutos; Nobuhiko Tanaka; Kazunori Waki; Yoshihiro Okuda; Tatsuya Kushida; Norio Kobayashi; Koji Doi; Kouji Kozaki; Robert Hoehndorf; Shigeharu Wakana; Tetsuro Toyoda; et al. (ICBO, 2011)

J-GLOBAL knowledge: Japan's Largest Linked Open Data for Science and Technology. - Takahiro Kimura; Takahiro Kawamura; Katsutaro Watanabe; Naoya Matsumoto; Tomonori Sato; Tatsuya Kushida; Katsuji Matsumura (ISWC (Posters & Demos), 2015)

Expanding Science and Technology Thesauri from Bibliographic Datasets Using Word Embedding. - Takahiro Kawamura; Kouji Kozaki; Tatsuya Kushida; Katsutaro Watanabe; Katsuji Matsumura (ICTAI, 2016)

Efficient Construction of a New Ontology for Life Sciences by Sub-classifying Related Terms in the Japan Science, Technology Agency Thesaurus. - Tatsuya Kushida; Kouji Kozaki; Yuka Tateisi; Katsutaro Watanabe; Takeshi Masuda; Katsuji Matsumura; Takahiro Kawamura; Toshihisa Takagi (ICBO, 2017)

Refined JST Thesaurus Extended with Data from Other Open Life Science Data Sources. - Tatsuya Kushida; Yuka Tateisi; Takeshi Masuda; Katsutaro Watanabe; Katsuji Matsumura; Takahiro Kawamura; Kouji Kozaki; Toshihisa Takagi (JIST, 2017)

Inference of Functions, Roles, and Applications of Chemicals Using Linked Open Data and Ontologies. - Tatsuya Kushida; Kouji Kozaki; Takahiro Kawamura; Yuka Tateisi; Yasunori Yamamoto; Toshihisa Takagi (JIST, 2018)

NBDC RDF portal: a comprehensive repository for semantic data in life sciences. - Shuichi Kawashima; Toshiaki Katayama; Hideki Hatanaka; Tatsuya Kushida; Toshihisa Takagi (Database J. Biol. Databases Curation, 2018)

Reconstruction of Hierarchical Structures in a Thesaurus-based Ontology through Curation by Domain Experts. - Tatsuya Kushida; Kouji Kozaki; Yasunori Yamamoto; Atsuko Yamaguchi; Takahiro Kawamura; Takako Nakagawa; Yuka Tateisi; Toshihisa Takagi (ICBO, 2019)

Building Knowledge Graph Across Different Subdomains Using Interlinking Ontology for Biomedical Concepts. - Kouji Kozaki; Tatsuya Kushida; Yasunori Yamamoto; Toshihisa Takagi (JIST (2), 2019)

Investigating Schema Definitions Using RDFS and OWL 2 for RDF Databases in Life Sciences. - Atsuko Yamaguchi; Tatsuya Kushida; Yasunori Yamamoto; Kouji Kozaki (JIST (2), 2019)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts. - Tatsuya Kushida; Kouji Kozaki; Takahiro Kawamura; Yuka Tateisi; Yasunori Yamamoto; Toshihisa Takagi (New Gener. Comput., 2019)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

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)

Ontology Integration for Discovering Bioresources Contributing to Medical Science Research. - Tatsuya Kushida; Daiki Usuda; Toyoyuki Takada; Yuki Yamagata; Hiroshi Masuya (ICBO, 2022)

Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets. - Tarcisio Mendes de Farias; Tatsuya Kushida; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frédéric B. Bastian; Hiroshi Masuya (SWAT4HCLS, 2023)

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)

Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. - Tatsuya Kushida; Tarcisio Mendes de Farias; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frederic B. Bastian; Hiroshi Masuya (BMC Medical Informatics Decis. Mak., 2025)