CyanoBase: the cyanobacteria genome database update 2010. - Mitsuteru Nakao; Shinobu Okamoto; Mitsuyo Kohara; Tsunakazu Fujishiro; Takatomo Fujisawa; Shusei Sato; Satoshi Tabata; Takakazu Kaneko; Yasukazu Nakamura (Nucleic Acids Res., 2010)

BioMart Central Portal: an open database network for the biological community. - Jonathan M. Guberman; Jiye Ai; Olivier Arnaiz; Joachim Baran; Andrew Blake 003; Richard A. Baldock; Claude Chelala; David Croft 001; Anthony Cros; Rosalind J. Cutts; Alex Di Génova; Simon A. Forbes; et al. (Database J. Biol. Databases Curation, 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; et al. (J. Biomed. Semant., 2011)

Semantic Integration of the Genome Annotations. - Toshiaki Katayama; Shinobu Okamoto; Shuichi Kawashima; Hiroshi Mori; Takatomo Fujisawa (SWAT4LS, 2012)

H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. - Eli Kaminuma; Takatomo Fujisawa; Yasuhiro Tanizawa; Naoko Sakamoto; Nori Kurata; Tokurou Shimizu; Yasukazu Nakamura (Nucleic Acids Res., 2013)

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; et al. (Nucleic Acids Res., 2014)

DDBJ progress report: a new submission system for leading to a correct annotation. - Takehide Kosuge; Jun Mashima; Yuichi Kodama; Takatomo Fujisawa; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura (Nucleic Acids Res., 2014)

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)

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)

The BioMart community portal: an innovative alternative to large, centralized data repositories. - Damian Smedley; Syed Haider; Steffen Durinck; Luca Pandini; Paolo Provero; James E. Allen; Olivier Arnaiz; Mohammad Hamza Awedh; Richard A. Baldock; Giulia Barbiera; Philippe Bardou; Tim Beck; et al. (Nucleic Acids Res., 2015)

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)

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)

CyanoBase: a large-scale update on its 20th anniversary. - Takatomo Fujisawa; Rei Narikawa; Shin-ichi Maeda; Satoru Watanabe; Yu Kanesaki; Koichi Kobayashi; Jiro Nomata; Mitsumasa Hanaoka; Mai Watanabe; Shigeki Ehira; Eiji Suzuki; Koichiro Awai; et al. (Nucleic Acids Res., 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)

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. - Yasuhiro Tanizawa; Takatomo Fujisawa; Yasukazu Nakamura (Bioinform., 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)

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)

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)

DDBJ Database updates and computational infrastructure enhancement. - Osamu Ogasawara; Yuichi Kodama; Jun Mashima; Takehide Kosuge; Takatomo Fujisawa (Nucleic Acids Res., 2020)

DDBJ update: streamlining submission and access of human data. - Asami Fukuda; Yuichi Kodama; Jun Mashima; Takatomo Fujisawa; Osamu Ogasawara (Nucleic Acids Res., 2021)

DNA Data Bank of Japan (DDBJ) update report 2021. - Toshihisa Okido; Yuichi Kodama; Jun Mashima; Takehide Kosuge; Takatomo Fujisawa; Osamu Ogasawara (Nucleic Acids Res., 2022)

Genome Variation Ontology for annotation of complex structural variations. - Shuichi Kawashima; Takatomo Fujisawa; Toshiaki Katayama (SWAT4HCLS, 2023)

To build densely connected Web of RDF data. - Yasunori Yamamoto; Takatomo Fujisawa (SWAT4HCLS, 2023)

DNA Data Bank of Japan (DDBJ) update report 2022. - Yasuhiro Tanizawa; Takatomo Fujisawa; Yuichi Kodama; Takehide Kosuge; Jun Mashima; Tomoya Tanjo; Yasukazu Nakamura (Nucleic Acids Res., 2023)

Make RDF data more inter-connectable. - Yasunori Yamamoto; Takatomo Fujisawa (SWAT4HCLS, 2024)

DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes. - Mohamed Elmanzalawi; Takatomo Fujisawa; Hiroshi Mori; Yasukazu Nakamura; Yasuhiro Tanizawa (BMC Bioinform., 2025)