CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses. - Akiko Hatano; Hirokazu Chiba; Harry Amri Moesa; Takeaki Taniguchi; Satoshi Nagaie; Koji Yamanegi; Takako Takai-Igarashi; Hiroshi Tanaka; Wataru Fujibuchi (Database J. Biol. Databases Curation, 2011)

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. - Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba (Nucleic Acids Res., 2013)

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. - Toshiaki Katayama; Mark D. Wilkinson; Kiyoko F. Aoki-Kinoshita; Shuichi Kawashima; Yasunori Yamamoto; Atsuko Yamaguchi; Shinobu Okamoto; Shin Kawano; Jin-Dong Kim; Yue Wang 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. - Hirokazu Chiba; Ikuo Uchiyama (BMC Bioinform., 2014)

SPANG: A Command-line Client Supporting Query Generation for Distributed SPARQL Endpoints. - Hirokazu Chiba; Ikuo Uchiyama (SWAT4LS, 2015)

Towards the Semantic Standardization of Orthology Content. - Jesualdo Tomás Fernández-Breis; María Del Carmen Legaz-García; Hirokazu Chiba; Ikuo Uchiyama (SWAT4LS, 2015)

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. - Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba (Nucleic Acids Res., 2015)

The Orthology Ontology: development and applications. - Jesualdo Tomás Fernández-Breis; Hirokazu Chiba; María Del Carmen Legaz-García; Ikuo Uchiyama (J. Biomed. Semant., 2016)

Leveraging Logical Rules for Efficacious Representation of Large Orthology Datasets. - Tarcisio M. Farias; Hirokazu Chiba; Jesualdo Tomás Fernández-Breis (SWAT4LS, 2017)

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. - Hirokazu Chiba; Ikuo Uchiyama (BMC Bioinform., 2017)

Mapping RDF Graphs to Property Graphs. - Shota Matsumoto; Ryota Yamanaka; Hirokazu Chiba (JIST (Workshops & Posters), 2018)

TogoGenome/TogoStanza: modularized Semantic Web genome database. - Toshiaki Katayama; Shuichi Kawashima; Shinobu Okamoto; Yuki Moriya; Hirokazu Chiba; Yuki Naito; Takatomo Fujisawa; Hiroshi Mori; Toshihisa Takagi (Database J. Biol. Databases Curation, 2019)

Property Graph Exchange Format. - Hirokazu Chiba; Ryota Yamanaka; Shota Matsumoto (CoRR, 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)

MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons. - Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba; Masaki Kato (Nucleic Acids Res., 2019)

SPANG: A SPARQL client with templating, one-liner functionality, and API. - Hirokazu Chiba (ISWC (Demos/Industry), 2020)

G2GML: Graph to Graph Mapping Language for Bridging RDF and Property Graphs. - Hirokazu Chiba; Ryota Yamanaka; Shota Matsumoto (ISWC (Demos/Industry), 2020)

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)

TogoID: an exploratory ID converter to bridge biological datasets. - Shuya Ikeda; Hiromasa Ono; Tazro Ohta; Hirokazu Chiba; Yuki Naito; Yuki Moriya; Shuichi Kawashima; Yasunori Yamamoto; Shinobu Okamoto; Susumu Goto; Toshiaki Katayama (Bioinform., 2022)

Formatting SPARQL 1.1 via Parsing Expression Grammar. - Hirokazu Chiba (IJCKG (Workshop/Poster/Demo), 2023)

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)

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)

Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features. - Shuya Ikeda; Kiyoko F. Aoki-Kinoshita; Hirokazu Chiba; Susumu Goto; Masae Hosoda; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Tazro Ohta; Hiromasa Ono; Terue Takatsuki; Yasunori Yamamoto; et al. (J. Biomed. Semant., 2025)