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

  • Yuichi Kodama
  • Eli Kaminuma
  • Satoshi Saruhashi
  • Kazuho Ikeo
  • Hideaki Sugawara
  • Yoshio Tateno
  • Yasukazu Nakamura
Conference paper

DOI: 10.1007/978-1-4419-5913-3_15

Volume 680 of the book series Advances in Experimental Medicine and Biology (AEMB)
Cite this paper as:
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

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.

Keywords

Biological database CIBEX DDBJ DDBJ omics archive DDBJ read annotation pipeline DDBJ read archive DDBJ trace archive Next-generation sequencing platform 

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

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Yuichi Kodama
  • Eli Kaminuma
  • Satoshi Saruhashi
  • Kazuho Ikeo
  • Hideaki Sugawara
  • Yoshio Tateno
    • 1
  • Yasukazu Nakamura
  1. 1.Center for Information Biology and DNA Data Bank of JapanNational Institute of GeneticsMishimaJapan