Satoshi Saruhashi

Publications of Satoshi Saruhashi

• Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies.

  Authors: Yuichi Kodama, Eli Kaminuma, Satoshi Saruhashi, Kazuho Ikeo, Hideaki Sugawara, Yoshio Tateno, Yasukazu Nakamura

  Advances in experimental medicine and biology. 01/2010; 680:125-35.

  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,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.

• DDBJ Sequence Read Archive / DDBJ Omics Archive

  Authors: Yuichi Kodama, Satoshi Saruhashi, Eli Kaminuma, Hideaki Sugawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura

  Nature Precedings.

  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 sequenceMassively 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.