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)

Genome Variation Ontology for annotation of complex structural variations - Shuichi Kawashima; Takatomo Fujisawa; Toshiaki Katayama (14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023, 2023)

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)

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)

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)

Med2RDF: Semantic Biomedical Knowledge-base and APIs for the Clinical Genome Medicine - Mayumi Kamada; Toshiaki Katayama; Shuichi Kawashima; Ryosuke Kojima; Masahiko Nakatsui; Yasushi Okuno (12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019)

Integrated Growth Media Database by Standardizing Ingredient Information - Shuichi Kawashima; Toshiaki Katayama; Yuki Moriya; Shinobu Okamoto; Yasunori Yamamoto; Susumu Goto (12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 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; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

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)

Construction of Knowledge-Base for Clinical Interpretation of Genomic Variants - Mayumi Kamada; Toshiaki Katayama; Shuichi Kawashima; Ryosuke Kojima; Masahiko Nakatsui; Yasushi Okuno (Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), Rome, Italy, December 4-7, 2017, 2017)

SPARQList: Markdown-Based Highly Configurable REST API Hosting Server for SPARQL - Toshiaki Katayama; Shuichi Kawashima (Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), Rome, Italy, December 4-7, 2017, 2017)

SPARQL-Proxy: A Generic Proxy Server for SPARQL Endpoint - Shuichi Kawashima; Toshiaki Katayama (Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), Rome, Italy, December 4-7, 2017, 2017)

Implementation of linked data in the life sciences at BioHackathon 2011 - Kiyoko F. Aoki-Kinoshita; Akira R. Kinjo; Mizuki Morita; Yoshinobu Igarashi; Yi-an Chen; Yasumasa Shigemoto; Takatomo Fujisawa; Yukie Akune; Takeo Katoda; Anna Kokubu; Takaaki Mori; Mitsuteru Nakao; et al. (J. Biomed. Semant., 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 (Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, Cambridge UK, December 7-10, 2015, 2015)

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; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list - Masaaki Kotera; Yosuke Nishimura; Zenichi Nakagawa; Ai Muto; Yuki Moriya; Shinobu Okamoto; Shuichi Kawashima; Toshiaki Katayama; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (J. Bioinform. Comput. Biol., 2014)

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters - Akihiro Nakaya; Toshiaki Katayama; Masumi Itoh; Kazushi Hiranuka; Shuichi Kawashima; Yuki Moriya; Shujiro Okuda; Michihiro Tanaka; Toshiaki Tokimatsu; Yoshihiro Yamanishi; Akiyasu C. Yoshizawa; Minoru Kanehisa; et al. (Nucleic Acids Res., 2013)

Global Well-Posedness in Critical Besov Spaces for Two-Fluid Euler-Maxwell Equations - Jiang Xu; Jun Xiong; Shuichi Kawashima (SIAM J. Math. Anal., 2013)

Decay Estimates of Solutions for Quasi-Linear Hyperbolic Systems of Viscoelasticity - Priyanjana M. N. Dharmawardane; Tohru Nakamura; Shuichi Kawashima (SIAM J. Math. Anal., 2012)

Dissipative Structure of the Regularity-Loss Type and Time Asymptotic Decay of Solutions for the Euler-Maxwell System - Yoshihiro Ueda; Shu Wang; Shuichi Kawashima (SIAM J. Math. Anal., 2012)

Semantic Integration of the Genome Annotations - Toshiaki Katayama; Shinobu Okamoto; Shuichi Kawashima; Hiroshi Mori; Takatomo Fujisawa (Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, Paris, France, November 28-30, 2012, 2012)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications - Toshiaki Katayama; Mark D. Wilkinson; Rutger A. Vos; Takeshi Kawashima; Shuichi Kawashima; Mitsuteru Nakao; Yasunori Yamamoto; Hong-Woo Chun; Atsuko Yamaguchi; Shin Kawano; Jan Aerts; Kiyoko F. Aoki-Kinoshita; et al. (J. Biomed. Semant., 2011)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009 - Hiroyuki Wakaguri; Yutaka Suzuki; Toshiaki Katayama; Shuichi Kawashima; Eri Kibukawa; Kazushi Hiranuka; Masahide Sasaki; Sumio Sugano; Junichi Watanabe (Nucleic Acids Res., 2009)

AAindex: amino acid index database, progress report 2008 - Shuichi Kawashima; Piotr Pokarowski; Maria Pokarowska; Andrzej Kolinski; Toshiaki Katayama; Minoru Kanehisa (Nucleic Acids Res., 2008)

KEGG for linking genomes to life and the environment - Minoru Kanehisa; Michihiro Araki; Susumu Goto; Masahiro Hattori; Mika Hirakawa; Masumi Itoh; Toshiaki Katayama; Shuichi Kawashima; Shujiro Okuda; Toshiaki Tokimatsu; Yoshihiro Yamanishi (Nucleic Acids Res., 2008)

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction - Zhenjun Hu; David M. Ng; Takuji Yamada; Chunnuan Chen; Shuichi Kawashima; Joe Mellor; Bolan Linghu; Minoru Kanehisa; Joshua M. Stuart; Charles DeLisi (Nucleic Acids Res., 2007)

From genomics to chemical genomics: new developments in KEGG - Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F. Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa (Nucleic Acids Res., 2006)

ODB: a database of operons accumulating known operons across multiple genomes - Shujiro Okuda; Toshiaki Katayama; Shuichi Kawashima; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2006)

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments - Ali Masoudi-Nejad; Koichiro Tonomura; Shuichi Kawashima; Yuki Moriya; Masanori Suzuki; Masumi Itoh; Minoru Kanehisa; Takashi Endo; Susumu Goto (Nucleic Acids Res., 2006)

The KEGG resource for deciphering the genome - Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Yasushi Okuno; Masahiro Hattori (Nucleic Acids Res., 2004)

The KEGG databases at GenomeNet - Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya (Nucleic Acids Res., 2002)

Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags - Takeshi Kawashima; Shuichi Kawashima; Yuji Kohara; Minoru Kanehisa; Kazuhiro W. Makabe (Nucleic Acids Res., 2002)

MAGEST: MAboya Gene Expression patterns and Sequence Tags - Takeshi Kawashima; Shuichi Kawashima; Minoru Kanehisa; Hiroki Nishida; Kazuhiro W. Makabe (Nucleic Acids Res., 2000)

AAindex: Amino Acid index database - Shuichi Kawashima; Minoru Kanehisa (Nucleic Acids Res., 2000)

AAindex: Amino Acid Index Database - Shuichi Kawashima; Hiroyuki Ogata; Minoru Kanehisa (Nucleic Acids Res., 1999)