Phenosite: a Web Database Integrating the mouse phenotyping Platform and the Experimental Procedures in mice. - Hiroshi Masuya; Sumi Yoshikawa; Naohiko Heida; Tetsuro Toyoda; Shigeharu Wakana; Toshihiko Shiroishi (J. Bioinform. Comput. Biol., 2007)

Objective Evaluation Measures of Genetic Marker Selection in Large-Scale SNP genotyping. - Eli Kaminuma; Hiroshi Masuya; Ikuo Miura; Hiromi Motegi; Kenzi R. Takahasi; Miki Nakazawa; Minami Matsui; Yoichi Gondo; Tetsuo Noda; Toshihiko Shiroishi; Shigeharu Wakana; Tetsuro Toyoda (J. Bioinform. Comput. Biol., 2008)

PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. - Yuko Yoshida; Yuko Makita; Naohiko Heida; Satomi Asano; Akihiro Matsushima; Manabu Ishii; Yoshiki Mochizuki; Hiroshi Masuya; Shigeharu Wakana; Norio Kobayashi; Tetsuro Toyoda (Nucleic Acids Res., 2009)

SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses. - Nobuhiko Tanaka; Kazunori Waki; Hideki Kaneda; Tomohiro Suzuki; Ikuko Yamada; Tamio Furuse; Kimio Kobayashi; Hiromi Motegi; Hideaki Toki; Maki Inoue; Osamu Minowa; Tetsuo Noda; et al. (Bioinform., 2010)

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)

The RIKEN integrated database of mammals. - Hiroshi Masuya; Yuko Makita; Norio Kobayashi; Koro Nishikata; Yuko Yoshida; Yoshiki Mochizuki; Koji Doi; Terue Takatsuki; Kazunori Waki; Nobuhiko Tanaka; Manabu Ishii; Akihiro Matsushima; et al. (Nucleic Acids Res., 2011)

Development of Linked Open Data for Bioresources. - Hiroshi Masuya; Terue Takatsuki; Yuko Makita; Yuko Yoshida; Yoshiki Mochizuki; Norio Kobayashi; Atsushi Yoshiki; Yukio Nakamura; Tetsuro Toyoda; Yuichi Obata (JIST, 2012)

An Ontology of Gene. - Hiroshi Masuya; Riichiro Mizoguchi (ICBO, 2012)

PosMed: A Biomedical Entity Prioritisation Tool Based on Statistical Inference over Literature and the Semantic Web. - Norio Kobayashi; Yuko Makita; Manabu Ishii; Akihiro Matsushima; Yoshiki Mochizuki; Koji Doi; Koro Nishikata; David Gifford 002; Terue Takatsuki; Hiroshi Masuya; Tetsuro Toyoda (SWAT4LS, 2013)

PosMed: ranking genes and bioresources based on Semantic Web Association Study. - Yuko Makita; Norio Kobayashi; Yuko Yoshida; Koji Doi; Yoshiki Mochizuki; Koro Nishikata; Akihiro Matsushima; Satoshi Takahashi; Manabu Ishii; Terue Takatsuki; Rinki Bhatia; Zolzaya Khadbaatar; et al. (Nucleic Acids Res., 2013)

CLO: The cell line ontology. - Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma D. Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Yue Liu; Terue Takatsuki; et al. (J. Biomed. Semant., 2014)

RIKEN Meta Database: A Life-science Metadata Database Based on the Semantic Web. - Norio Kobayashi; Kai Lenz; Hiroshi Masuya (SWAT4LS, 2015)

RDF-based Data Sharing of Bio-resource Related Information. - Hiroshi Masuya; Terue Takatsuki; Mikako Saito; Eiki Takayama; Kazuya Ohshima; Nozomu Ohshiro; Kai Lenz; Nobuhiko Tanaka; Hiroshi Mori; Shuichi Kawashima; Norio Kobayashi (SWAT4LS, 2015)

RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences. - Norio Kobayashi; Kai Lenz; Hiroshi Masuya (JIST (Workshops & Posters), 2016)

Semantic Data Acquisition by Traversing Class-Class Relationships Over Linked Open Data. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (JIST, 2016)

SPARQL Builder: Constructing SPARQL Query by Traversing Class-Class Relationships for Life Science Databases. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (JIST (Workshops & Posters), 2016)

Development of an Ontology for an Integrated Image Analysis Platform to enable Global Sharing of Microscopy Imaging Data. - Satoshi Kume; Hiroshi Masuya; Yosky Kataoka; Norio Kobayashi (ISWC (Posters & Demos), 2016)

RIKEN MetaDatabase: a Database Publication Platform for RIKENs Life-science Researchers that Promotes Research Collaborations over Different Research Area. - Kai Lenz; Hiroshi Masuya; Norio Kobayashi (ISWC (Posters & Demos), 2016)

A RDF based Portal of Biological Phenotype Data produced in Japan. - Terue Takatsuki; Mikako Saito; Sadahiro Kumagai; Eiki Takayama; Kazuya Ohshima; Nozomu Ohshiro; Kai Lenz; Nobuhiko Tanaka; Norio Kobayashi; Hiroshi Masuya (ISWC (Posters & Demos), 2016)

Data Acquisition by Traversing Class-Class Relationships over the Linked Open Data. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (ISWC (Posters & Demos), 2016)

SPARQL Query Construction with Monitoring Service for Endpoints. - Atsuko Yamaguchi; Yasunori Yamamoto; Kouji Kozaki; Kai Lenz; Hiroshi Masuya; Norio Kobayashi (SWAT4LS, 2016)

Development of Semantic Web-Based Imaging Database for Biological Morphome. - Satoshi Kume; Hiroshi Masuya; Mitsuyo Maeda; Mitsuo Suga; Yosky Kataoka; Norio Kobayashi (JIST, 2017)

Semantic Graph Analysis for Federated LOD Surfing in Life Sciences. - Atsuko Yamaguchi; Kouji Kozaki; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (JIST, 2017)

Metadata-driven Interdisciplinary Research Projects Using RIKEN MetaDatabase. - Norio Kobayashi; Satoshi Kume; Hiroshi Masuya (SWAT4LS, 2017)

LOD Surfer API: Web API for LOD Surfing Using Class-Class Relationships in Life Sciences. - Atsuko Yamaguchi; Kouji Kozaki; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (SWAT4LS, 2017)

RIKEN MetaDatabase: A Database Platform for Health Care and Life Sciences as a Microcosm of Linked Open Data Cloud. - Norio Kobayashi; Satoshi Kume; Kai Lenz; Hiroshi Masuya (Int. J. Semantic Web Inf. Syst., 2018)

Soft windowing application to improve analysis of high-throughput phenotyping data. - Hamed Haselimashhadi; Jeremy C. Mason; Violeta Muñoz-Fuentes; Federico López-Gómez; Kolawole O. Babalola; Elif F. Acar; Vivek Kumar; Jacqui White; Ann M. Flenniken; Ruairidh King; Ewan Straiton; John Richard Seavitt; et al. (Bioinform., 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)

Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology. - Yuki Yamagata; Shuichi Onami; 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)