Yuichi Kodama

Publications of Yuichi Kodama

• The Sequence Read Archive: explosive growth of sequencing data.

  Authors: Yuichi Kodama, Martin Shumway, Rasko Leinonen

  Nucleic acids research. 01/2012; 40(Database issue):D54-6.

  New generation sequencing platforms are producing data with significantly higher throughput and lower cost. A portion of this capacity is devoted to individual and community scientific projects. AsNew generation sequencing platforms are producing data with significantly higher throughput and lower cost. A portion of this capacity is devoted to individual and community scientific projects. As these projects reach publication, raw sequencing datasets are submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). Archiving experimental data is the key to the progress of reproducible science. The SRA was established as a public repository for next-generation sequence data as a part of the International Nucleotide Sequence Database Collaboration (INSDC). INSDC is composed of the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at www.ncbi.nlm.nih.gov/sra from NCBI, at www.ebi.ac.uk/ena from EBI and at trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA and report on updated metadata structures, submission file formats and supported sequencing platforms. We also briefly outline our various responses to the challenge of explosive data growth.

• The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

  Authors: Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura

  Nucleic acids research. 11/2011; 40(Database issue):D38-42.

  The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists ofThe DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

• DDBJ progress report.

  Authors: Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura

  Nucleic acids research. 11/2010; 39(Database issue):D22-7.

  The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotationThe DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3,637,446 entries/2,272,231,889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing reads of Japanese rice cultivar, Koshihikari submitted by the National Institute of Agrobiological Sciences. In this period, we started a new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline. In this article, we describe these new functions of the DDBJ databases and support tools.

• 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 launches a new archive database with analytical tools for next-generation sequence data.

  Authors: Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura

  Nucleic acids research. 10/2009;

  The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has collected and released 1 701 110 entries/1 116 138 614 bases between July 2008 and June 2009. A few highlighted data releases fromThe DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has collected and released 1 701 110 entries/1 116 138 614 bases between July 2008 and June 2009. A few highlighted data releases from DDBJ were the complete genome sequence of an endosymbiont within protist cells in the termite gut and Cap Analysis Gene Expression tags for human and mouse deposited from the Functional Annotation of the Mammalian cDNA consortium. In this period, we started a novel user announcement service using Really Simple Syndication (RSS) to deliver a list of data released from DDBJ on a daily basis. Comprehensive visualization of a DDBJ release data was attempted by using a word cloud program. Moreover, a new archive for sequencing data from next-generation sequencers, the 'DDBJ Read Archive' (DRA), was launched. Concurrently, for read data registered in DRA, a semi-automatic annotation tool called the 'DDBJ Read Annotation Pipeline' was released as a preliminary step. The pipeline consists of two parts: basic analysis for reference genome mapping and de novo assembly and high-level analysis of structural and functional annotations. These new services will aid users' research and provide easier access to DDBJ databases.

• DDBJ Activities: Contribution to the Research in Information Biology

  Authors: Jun Mashima, Takehide Kosuge, Toshihisa Okido, Yuichi Kodama, Kazuho Ikeo, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori

  Nature Precedings.

  DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International NucleotideDDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also collecting and releasing gene expression data at CIBEX (Center for Information Biology gene EXpression database; "http://cibex.nig.ac.jp/":http://cibex.nig.ac.jp/). Furthermore, DDBJ contributed to international annotation jamborees such as FANTOM (mouse), H-Inv (human), RAP (rice) and E. coli K12. DDBJ provides many services to the research in information biology or bioinformatics. They include Web-API for Biology (WABI) "http://www.xml.nig.ac.jp/":http://www.xml.nig.ac.jp/ and All-round Retrieval of Sequence and Annotation (ARSA) "http://arsa.ddbj.nig.ac.jp/":http://arsa.ddbj.nig.ac.jp/. These activities are presented with the perspective of DDBJ in the coming years.

• 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.