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

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Advances in Computational Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 680))

Abstract

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.

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Abbreviations

CIB-DDBJ:

Center for Information Biology and DDBJ

CIBEX:

Center for Information Biology gene EXpression database

DDBJ:

DNA Data Bank of Japan

DOR:

DDBJ Omics aRchive

DRA:

DDBJ Read Archive

DTA:

DDBJ Trace Archive

EBI:

European Bioinformatics Institute

EMBL:

European Molecular Biology Laboratory

ERA:

European Read Archive

GEO:

Gene Expression Omnibus

INSDC:

International Nucleotide Sequence Database Collaboration

MGED:

Microarray Gene Expression Data

MIAME:

Minimum Information About a Microarray Experiment

MINSEQE:

Minimum Information about a high-throughput Nucleotide SEQuencing Experiment

NCBI:

National Center for Biotechnology Information

SRA:

Short Read Archive

UHTS:

Ultra High-Throughput Sequencing

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Acknowledgments

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 (http://lifesciencedb.mext.go.jp/en) by MEXT and by the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency.

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Authors and Affiliations

  1. Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan

    Yoshio Tateno

Authors
  1. Yuichi Kodama
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  2. Eli Kaminuma
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  3. Satoshi Saruhashi
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  4. Kazuho Ikeo
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  5. Hideaki Sugawara
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  6. Yoshio Tateno
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  7. Yasukazu Nakamura
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Corresponding author

Correspondence to Yoshio Tateno .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of Georgia, Athens, 30602-7404, Georgia, USA

    Hamid R. Arabnia

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Kodama, Y. et al. (2010). Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies. In: Arabnia, H. (eds) Advances in Computational Biology. Advances in Experimental Medicine and Biology, vol 680. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5913-3_15

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