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

被引:26
作者
Kodama, Yuichi
Mashima, Jun
Kaminuma, Eli
Gojobori, Takashi
Ogasawara, Osamu
Takagi, Toshihisa
Okubo, Kousaku
Nakamura, Yasukazu [1 ]
机构
[1] Res Org Informat & Syst, Natl Inst Genet, Ctr Informat Biol, Mishima, Shizuoka 4118510, Japan
关键词
CIONA-INTESTINALIS; STANDARDS; CHORDATE;
D O I
10.1093/nar/gkr994
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 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.
引用
收藏
页码:D38 / D42
页数:5
相关论文
共 11 条
[1]   NCBI GEO: archive for functional genomics data sets-10 years on [J].
Barrett, Tanya ;
Troup, Dennis B. ;
Wilhite, Stephen E. ;
Ledoux, Pierre ;
Evangelista, Carlos ;
Kim, Irene F. ;
Tomashevsky, Maxim ;
Marshall, Kimberly A. ;
Phillippy, Katherine H. ;
Sherman, Patti M. ;
Muertter, Rolf N. ;
Holko, Michelle ;
Ayanbule, Oluwabukunmi ;
Yefanov, Andrey ;
Soboleva, Alexandra .
NUCLEIC ACIDS RESEARCH, 2011, 39 :D1005-D1010
[2]   Minimum information about a microarray experiment (MIAME) - toward standards for microarray data [J].
Brazma, A ;
Hingamp, P ;
Quackenbush, J ;
Sherlock, G ;
Spellman, P ;
Stoeckert, C ;
Aach, J ;
Ansorge, W ;
Ball, CA ;
Causton, HC ;
Gaasterland, T ;
Glenisson, P ;
Holstege, FCP ;
Kim, IF ;
Markowitz, V ;
Matese, JC ;
Parkinson, H ;
Robinson, A ;
Sarkans, U ;
Schulze-Kremer, S ;
Stewart, J ;
Taylor, R ;
Vilo, J ;
Vingron, M .
NATURE GENETICS, 2001, 29 (04) :365-371
[3]   Evidence standards in experimental and inferential INSDC Third Party Annotation data [J].
Cochrane, Guy ;
Bates, Kirsty ;
Apweiler, Rolf ;
Tateno, Yoshio ;
Mashima, Jun ;
Kosuge, Takehide ;
Mizrachi, Ilene Karsch ;
Schafer, Susan ;
Fetchko, Michael .
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 2006, 10 (02) :105-113
[4]   The draft genome of Ciona intestinalis:: Insights into chordate and vertebrate origins [J].
Dehal, P ;
Satou, Y ;
Campbell, RK ;
Chapman, J ;
Degnan, B ;
De Tomaso, A ;
Davidson, B ;
Di Gregorio, A ;
Gelpke, M ;
Goodstein, DM ;
Harafuji, N ;
Hastings, KEM ;
Ho, I ;
Hotta, K ;
Huang, W ;
Kawashima, T ;
Lemaire, P ;
Martinez, D ;
Meinertzhagen, IA ;
Necula, S ;
Nonaka, M ;
Putnam, N ;
Rash, S ;
Saiga, H ;
Satake, M ;
Terry, A ;
Yamada, L ;
Wang, HG ;
Awazu, S ;
Azumi, K ;
Boore, J ;
Branno, M ;
Chin-bow, S ;
DeSantis, R ;
Doyle, S ;
Francino, P ;
Keys, DN ;
Haga, S ;
Hayashi, H ;
Hino, K ;
Imai, KS ;
Inaba, K ;
Kano, S ;
Kobayashi, K ;
Kobayashi, M ;
Lee, BI ;
Makabe, KW ;
Manohar, C ;
Matassi, G ;
Medina, M .
SCIENCE, 2002, 298 (5601) :2157-2167
[5]   DDBJ progress report [J].
Kaminuma, Eli ;
Kosuge, Takehide ;
Kodama, Yuichi ;
Aono, Hideo ;
Mashima, Jun ;
Gojobori, Takashi ;
Sugawara, Hideaki ;
Ogasawara, Osamu ;
Takagi, Toshihisa ;
Okubo, Kousaku ;
Nakamura, Yasukazu .
NUCLEIC ACIDS RESEARCH, 2011, 39 :D22-D27
[6]   The International Nucleotide Sequence Database Collaboration [J].
Karsch-Mizrachi, Ilene ;
Nakamura, Yasukazu ;
Cochrane, Guy .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D33-D37
[7]   The sequence read archive: explosive growth of sequencing data [J].
Kodama, Yuichi ;
Shumway, Martin ;
Leinonen, Rasko .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D54-D56
[8]   Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies [J].
Kodama, Yuichi ;
Kaminuma, Eli ;
Saruhashi, Satoshi ;
Ikeo, Kazuho ;
Sugawara, Hideaki ;
Tateno, Yoshio ;
Nakamura, Yasukazu .
ADVANCES IN COMPUTATIONAL BIOLOGY, 2010, 680 :125-135
[9]   Web API for biology with a workflow navigation system [J].
Kwon, Yeondae ;
Shigemoto, Yasumasa ;
Kuwana, Yoshikazu ;
Sugawara, Hideaki .
NUCLEIC ACIDS RESEARCH, 2009, 37 :W11-W16
[10]   ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments [J].
Parkinson, Helen ;
Sarkans, Ugis ;
Kolesnikov, Nikolay ;
Abeygunawardena, Niran ;
Burdett, Tony ;
Dylag, Miroslaw ;
Emam, Ibrahim ;
Farne, Anna ;
Hastings, Emma ;
Holloway, Ele ;
Kurbatova, Natalja ;
Lukk, Margus ;
Malone, James ;
Mani, Roby ;
Pilicheva, Ekaterina ;
Rustici, Gabriella ;
Sharma, Anjan ;
Williams, Eleanor ;
Adamusiak, Tomasz ;
Brandizi, Marco ;
Sklyar, Nataliya ;
Brazma, Alvis .
NUCLEIC ACIDS RESEARCH, 2011, 39 :D1002-D1004