Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies

  • Yuichi Kodama
  • Eli Kaminuma
  • Satoshi Saruhashi
  • Kazuho Ikeo
  • Hideaki Sugawara
  • Yoshio Tateno
  • Yasukazu Nakamura
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 680)


The Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) has operated biological databases since 1987 in collaboration with NCBI and EBI. As one of the three major public databases, CIB-DDBJ has run four primary databases DDBJ, CIBEX, DDBJ Trace Archive (DTA), and DDBJ Read Archive (DRA) to collect, archive, and provide various kinds of biological data. As the massively parallel new sequencing platforms are increasingly in use, huge amounts of the raw data have been produced. To archive these raw data, we at CIB-DDBJ began operating a new repository, the DDBJ Read Archive (DRA). To accommodate efficiently the processed data as well, we have developed a new pipeline, the DDBJ Read Annotation Pipeline that deals with both data submission and analysis. For data produced by the next generation platforms, the three archives DRA, DDBJ, and CIBEX, which are interconnected by the pipeline, collect the raw, processed sequence, and quantitative data, respectively. The public biological databases at CIB-DDBJ, EBI, and NCBI will together construct world-wide archives for biological data by data sharing to accelerate research in life sciences in the era of next generation sequencing technologies.


Biological database CIBEX DDBJ DDBJ omics archive DDBJ read annotation pipeline DDBJ read archive DDBJ trace archive Next-generation sequencing platform 



Center for Information Biology and DDBJ


Center for Information Biology gene EXpression database


DNA Data Bank of Japan


DDBJ Omics aRchive


DDBJ Read Archive


DDBJ Trace Archive


European Bioinformatics Institute


European Molecular Biology Laboratory


European Read Archive


Gene Expression Omnibus


International Nucleotide Sequence Database Collaboration


Microarray Gene Expression Data


Minimum Information About a Microarray Experiment


Minimum Information about a high-throughput Nucleotide SEQuencing Experiment


National Center for Biotechnology Information


Short Read Archive


Ultra High-Throughput Sequencing



We gratefully acknowledge the support of all members of CIB-DDBJ. In particular, we thank Takako Mochizuki for constructing the pipeline. We also especially thank Daisuke Fukuda, Keisuke Yamamoto, Wataru Kodachi, and Masahiro Fujimoto for DRA development; Toshinori Yagi for the development of CIBEX; and Drs. Takashi Gojobori, Toshihisa Takagi, and Kousaku Okubo for their supports and understandings.

DDBJ is funded by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan with a management expenses grant for national university cooperation. The DDBJ Read Archive and DDBJ Trace Archive are supported partially by the Integrated Database Project ( by MEXT and by the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency.


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Yuichi Kodama
  • Eli Kaminuma
  • Satoshi Saruhashi
  • Kazuho Ikeo
  • Hideaki Sugawara
  • Yoshio Tateno
    • 1
  • Yasukazu Nakamura
  1. 1.Center for Information Biology and DNA Data Bank of JapanNational Institute of GeneticsMishimaJapan

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