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. 2017 Jan 4;45(D1):D25-D31.
doi: 10.1093/nar/gkw1001. Epub 2016 Oct 24.

DNA Data Bank of Japan

Jun Mashima  1 , Yuichi Kodama  2 , Takatomo Fujisawa  2 , Toshiaki Katayama  3 , Yoshihiro Okuda  2 , Eli Kaminuma  2 , Osamu Ogasawara  2 , Kousaku Okubo  2 , Yasukazu Nakamura  2 , Toshihisa Takagi  4   5
Affiliations

DNA Data Bank of Japan

Jun Mashima et al. Nucleic Acids Res. .

Abstract

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data.

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Figures

Figure 1.
Figure 1.
Improvement to link ICTV records on the viral taxonomic records of TXSearch tool. (A) Schematic diagram of data flow to insert links to ICTV records into NCBI Taxonomy records. (B) Screenshot of a viral record on TXSearch tool. The red arrow shows a link to the ICTV record.
See this image and copyright information in PMC

References

    1. Mashima J., Kodama Y., Kosuge T., Fujisawa T., Katayama T., Nagasaki H., Okuda Y., Kaminuma E., Ogasawara O., Okubo K., et al. DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res. 2016;44:D51–D57. - PMC - PubMed
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    1. Cochrane G., Karsch-Mizrachi I., Takagi T. The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2016;44:D48–D50. - PMC - PubMed
    1. Kosuge T., Mashima J., Kodama Y., Fujisawa T., Kaminuma E., Ogasawara O., Okubo K., Takagi T., Nakamura Y. DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res. 2014;42:D44–D49. - PMC - PubMed

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