Toshiaki Katayama

According to our database, Toshiaki Katayama authored at least 44 papers between 2005 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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, Toshiaki Katayama

J. Biomed. Semant., December, 2025

2023

Genome Variation Ontology for annotation of complex structural variations.

Shuichi Kawashima, Takatomo Fujisawa, Toshiaki Katayama

Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

2022

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

2020

Ten simple rules to run a successful BioHackathon.

Leyla J. García, Erick Antezana, Alexander García Castro, Evan Bolton, Rafael C. Jiménez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama

PLoS Comput. Biol., 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, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

F1000Research, 2020

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, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi

F1000Research, 2019

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

Integrated Growth Media Database by Standardizing Ingredient Information.

Shuichi Kawashima, Toshiaki Katayama, Yuki Moriya, Shinobu Okamoto, Yasunori Yamamoto, Susumu Goto

Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

MetaStanza: Generic WebComponents Widgets for Visualizing SPARQL Results on the Web.

Toshiaki Katayama

Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 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

Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

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

2017

DNA Data Bank of Japan.

Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi

Nucleic Acids Res., 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), 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), 2017

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), 2017

2016

DNA data bank of Japan (DDBJ) progress report.

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi

Nucleic Acids Res., 2016

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul Jean Pierre Bonnal, Robert M. Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock

J. Biomed. Semant., 2016

2015

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data.

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura

Nucleic Acids Res., 2015

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, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama, Soichi Ogishima

J. Biomed. Semant., 2015

SPARQL-enabled identifier conversion with Identifiers.org.

Sarala M. Wimalaratne, Jerven T. Bolleman, Nick S. Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novère, Henning Hermjakob, Camille Laibe

Bioinform., 2015

D2RQ Mapper.

Yasunori Yamamoto, Toshiaki Katayama

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

2014

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

Shin Kawano, Tsutomu Watanabe, Sohei Mizuguchi, Norie Araki, Toshiaki Katayama, Atsuko Yamaguchi

Nucleic Acids Res., 2014

CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.

Takatomo Fujisawa, Shinobu Okamoto, Toshiaki Katayama, Mitsuteru Nakao, Hidehisa Yoshimura, Hiromi Kajiya-Kanegae, Sumiko Yamamoto, Chiyoko Yano, Yuka Yanaka, Hiroko Maita, Takakazu Kaneko, Satoshi Tabata, Yasukazu Nakamura

Nucleic Acids Res., 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

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Steffen Möller, Enis Afgan, Michael Banck, Raoul Jean Pierre Bonnal, Timothy Booth, John Chilton, Peter J. A. Cock, Markus Gumbel, Nomi L. Harris, Richard C. G. Holland, Matús Kalas, László Kaján, Eri Kibukawa, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Guimera, Toshiaki Katayama, Brad A. Chapman

BMC Bioinform., 2014

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, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-an Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin

J. Biomed. Semant., 2014

D3SPARQL: JavaScript Library for Visualization of SPARQL Results.

Toshiaki Katayama

Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014

2013

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, Susumu Goto

Nucleic Acids Res., 2013

Interactive Platform for Semantic Gene Expression Analysis of Alzheimer's Disease.

Toshiaki Katayama, Masataka Kikuchi, Soichi Ogishima

Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2013

2012

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

Hiroyuki Mishima, Jan Aerts, Toshiaki Katayama, Raoul Jean Pierre Bonnal, Koh-ichiro Yoshiura

BMC Bioinform., 2012

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Raoul Jean Pierre Bonnal, Jan Aerts, George Githinji, Naohisa Goto, Daniel MacLean, Chase A. Miller, Hiroyuki Mishima, Massimiliano Pagani, Ricardo Ramirez-Gonzalez, Geert Smant, Francesco Strozzi, Rob Syme, Rutger A. Vos, Trevor J. Wennblom, Ben J. Woodcroft, Toshiaki Katayama, Pjotr Prins

Bioinform., 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, 2012

2011

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, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

J. Biomed. Semant., 2011

BioMart Central Portal: an open database network for the biological community.

Jonathan M. Guberman, Jiye Ai, Olivier Arnaiz, Joachim Baran, Andrew Blake, Richard A. Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, Alex Di Génova, Simon A. Forbes, Takatomo Fujisawa, Emanuela Gadaleta, David M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd W. Harris, Robin Haw, Shen Hu, Simon J. Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, Rhoda Kinsella, Lei Kong, Daniel Lawson, Yong Liang, Núria López-Bigas, Jie Luo, Michael J. Lush, Jeremy C. Mason, François Moreews, Nelson Ndegwa, Darren J. Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, Steven Rosanoff, Rebecca Shepherd, Reinhard Simon, William C. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin R. Stone, Jon W. Teague, Jun Wang, Jianxin Wang, Brett Whitty, David Tai Wai Wong, Marie Wong-Erasmus, Long Yao, Ken Youens-Clark, Christina K. Yung, Junjun Zhang, Arek Kasprzyk

Database J. Biol. Databases Curation, 2011

2010

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services.

Toshiaki Katayama, Mitsuteru Nakao, Toshihisa Takagi

Nucleic Acids Res., 2010

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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

J. Biomed. Semant., 2010

BioRuby: bioinformatics software for the Ruby programming language.

Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Jean Pierre Bonnal, Jan Aerts, Toshiaki Katayama

Bioinform., 2010

2009

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

2008

KEGG Atlas mapping for global analysis of metabolic pathways.

Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa

Nucleic Acids Res., 2008

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

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

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

2005

Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.

Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano

J. Bioinform. Comput. Biol., 2005