Biocuration 2010

DDBJ Sequence Read Archive / DDBJ Omics Archive

Abstract

Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields. DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI. In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms. DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy. Since 2004, DDBJ has operated CIBEX as a repository database for the microarray data. In 2009, we decided to establish a new archive DDBJ Omics Archive (DOR) to efficiently accommodate the massive amounts of quantitative data. DOR integrates array-based CIBEX data. DOR accepts submissions of functional genomics data both from the array- and sequencing-based platforms in collaboration with EBI ArrayExpress. DOR uses the same standards with those of ArrayExpress, namely, MAGE-TAB file format for metadata, MIAME and MINSEQE guidelines for submissions. Thus, the data sets released from DOR are seamlessly exported to ArrayExpress. Moreover, entrances of the submission is unified between the DOR and DRA, in which the submitters once deposit their raw and processed data with necessary metadata, their data will be registered to both databases.DDBJ continues to serve the biological science with the primary archive databases of DDBJ, DRA and DOR.

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Nakamura, Y., Kodama, Y., Saruhashi, S. et al. DDBJ Sequence Read Archive / DDBJ Omics Archive. Nat Prec (2010). https://doi.org/10.1038/npre.2010.5085.1

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Keywords

  • DDBJ
  • database
  • curation
  • DDBJ Sequence Read Archive
  • DDBJ Omics Archive