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DNA Data Bank of Japan

Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2016 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ) (http://www. ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987).  ...  We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc. org), in collaboration with the  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for  ... 
doi:10.1093/nar/gkw1001 pmid:27924010 pmcid:PMC5210514 fatcat:sbslos5mnbgnpfurvzabh2svki

DNA Data Bank of Japan: 30th anniversary

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2017 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ) Center (http: //www.ddbj.nig.ac.jp) has been providing public data services for 30 years since 1987.  ...  Furthermore, we highlight our responses to the amended Japanese rules for the protection of personal information and the launch of the DDBJ Group Cloud service for sharing pre-publication data among research  ...  INTRODUCTION The DNA Data Bank of Japan (DDBJ, http://www.ddbj. nig.ac.jp) (1) is a public database of nucleotide sequences established at the National Institute of Genetics (NIG, https: //www.nig.ac.jp  ... 
doi:10.1093/nar/gkx926 pmid:29040613 pmcid:PMC5753283 fatcat:3n45p6fz6bcfzgtv6j2prd44vq

DNA Data Bank of Japan (DDBJ) in XML

S. Miyazaki
2003 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ, http:// www.ddbj.nig.ac.jp) has collected and released more entries and bases than last year.  ...  The contributions of DDBJ over the past year are 17.3% (entries) and 10.3% (bases) of the combined outputs of the International Nucleotide Sequence Databases (INSD).  ...  ACKNOWLEDGEMENTS We thank the DDBJ members for making it possible to run DDBJ well in collaboration with EMBL Bank and GenBank.  ... 
doi:10.1093/nar/gkg088 pmid:12519938 pmcid:PMC165535 fatcat:yidibr4vkjbhtazo425ipn46ie

DNA data bank of Japan (DDBJ) progress report

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2015 Nucleic Acids Research  
The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DB-CLS) in Japan.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for their assistance in data collection, annotation, release, and software development  ... 
doi:10.1093/nar/gkv1105 pmid:26578571 pmcid:PMC4702806 fatcat:dsvzn2iivjb7jhqnqhoehswhtu

DNA Data Bank of Japan at work on genome sequence data

Y Tateno
1998 Nucleic Acids Research  
We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp ) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome projects.  ...  This system (http://mol.genes.nig.ac.jp/ ecoli/ ) can in theory be used for any genome sequence data. These activities will facilitate processing of large quantities of EST and genome data.  ...  INSD is a tripartite international collaboration between the EMBL Nucleotide Sequence Database, GenBank and the DNA Data Bank of Japan (DDBJ).  ... 
doi:10.1093/nar/26.1.16 pmid:9399792 pmcid:PMC147185 fatcat:5gln47g55fhudcoqzobyalkequ

DNA Data Bank of Japan dealing with large-scale data submission

H. Sugawara, S. Miyazaki, T. Gojobori, Y. Tateno
1999 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ) (http//:www. ddbj.nig.ac.jp ) has developed a software system for mass submissions to cope with a recent expansion of EST and genome data submissions.  ...  DDBJ has received large scale data of Homo sapiens, Arabidopsis and Pyrococcus from Japanese researchers who made full use of the new submission system.  ...  INTRODUCTION When we began data bank activity at the DNA Data Bank of Japan (DDBJ) (http//:www.ddbj.nig.ac.jp ) more than 10 years ago, we expected that the amount of submitted data would double over the  ... 
doi:10.1093/nar/27.1.25 pmid:9847134 pmcid:PMC148089 fatcat:zkf63jqknzgmjd6v5pzn6lyiai

Visualization of Sequence and Biological Data in DNA Data Bank of Japan

Kousuke Goto, Toshitsugu Okayama, Hirotada Mori, Hikaru Yamamoto, Tomohiro Koike, Takashi Gojobori, Takuro Tamura, Satoru Miyazaki, Hideaki Sugawara
1997 Genome Informatics Series  
Data submitters, reviewers and users of DNA Data Bank of Japan (DDBJ) processes sequence data longer than 1M base pairs thanks to genome projects.  ...  A newly developed data dissemination system named Genome Information Broker and the enhancement of Web data submission system SAKURA are introduced here from the viewpoint of visualization.  ...  Therefore, it is obvious that the data bank and the user require a tool which provides a comprehensive view of a mega sequence like a genome sequence.  ... 
doi:10.11234/gi1990.8.236 fatcat:oe4gffumlnclzc63flwq7lzmlu

DNA Data Bank of Japan in the age of information biology

Y. Tateno, T. Gojobori
1997 Nucleic Acids Research  
DNA Data Bank of Japan (DDBJ) began its activities in 1986 in collaboration with EMBL in Europe and GenBank in the United States.  ...  The data bank also built a database management system (Yamato II), incorporating the techniques and functions of the object-oriented database, in order to efficiently process the data it has collected.  ...  INTRODUCTION The DNA Data Bank of Japan (DDBJ) began its activities in earnest in 1986 in collaboration with EMBL and GenBank.  ... 
doi:10.1093/nar/25.1.14 pmid:9016494 pmcid:PMC146410 fatcat:fz6zk7shondftb2plfd7gftf54

DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams

Y. Tateno
2000 Nucleic Acids Research  
It is emphasised that the collaboration between data producing teams and the data bank is crucial in carrying out these processes smoothly.  ...  To cope with this situation, we have developed tools not only for processing such massive amounts of data but also for efficiently retrieving data on demand.  ...  Hashimoto of DDBJ for their contributions to the present report.  ... 
doi:10.1093/nar/28.1.24 pmid:10592172 pmcid:PMC102400 fatcat:naqluyolf5blnny7ofrspgsvsa

DNA Data Bank of Japan (DDBJ) for genome scale research in life science

Y. Tateno
2002 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ, http:// www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from Japanese researchers.  ...  The increase rates of the data we collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases.  ...  ACKNOWLEDGEMENTS We thank the rest of the DDBJ members for making it possible to run well this international DNA data bank.  ... 
doi:10.1093/nar/30.1.27 pmid:11752245 pmcid:PMC99140 fatcat:jwasybhs2bgqnf7bqnjczxzrsi

Applications based on object oriented technology at DNA Data Bank of JAPAN(DDBJ)
日本DNAデータバンクにおけるオブジェクト指向技術の活用

2001 Joho Chishiki Gakkaishi  
り塩 基配 列 デ ー タ ベ ー ス の 開発 に 着手 し 、 日 本 DNA デ ー タ バ ン ク ( DNA Data Bank of JAPAN , 以 下 DDBJ ) と し て 国 際的 な 事 業 を展 開 し て い る 。  ...  Nuclieci Acids Research , pp25 − 28 , VQL 27 , N o . 1 , 1999 [ 3 ] DNA Data Bank of Japan ( DDBJ ) in collaboration with mass sequencing teams .  ... 
doi:10.2964/jsik_kj00001039354 fatcat:dqe27gb4ifgmnbyalcdf6655vm

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

Y. Kodama, J. Mashima, E. Kaminuma, T. Gojobori, O. Ogasawara, T. Takagi, K. Okubo, Y. Nakamura
2011 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ; http://www .ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information.  ...  DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of DDBJ for data collection, annotation and release and for software development.  ... 
doi:10.1093/nar/gkr994 pmid:22110025 pmcid:PMC3244990 fatcat:kbjrao6jw5hnrc4tcpq767mgsi

Whole genome sequencing data of Vigna nakashimae var. Ukushima and G418

Eri Ogiso-Tanaka, Sompong Chankaew, Takehisa Isemura, Alisa Kongjaimun, Akiko Baba, Ken Naito, Akito Kaga, Norihiko Tomooka
2020 Data in Brief  
NGS data was deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA009307.  ...  Two strain of 'Ukushima' and 'G418' were identified as salt tolerance strains in Vigna nakashimae from gene bank collection.  ...  Acknowledgments Support for the work of EOT was provided by JSPS KAKENHI Grant Number 25871107.  ... 
doi:10.1016/j.dib.2020.105131 pmid:32021887 pmcid:PMC6994819 fatcat:z3aczin33bdgpcbhysjtcswoqa

Draft genome sequence of Japanese pear (Pyrus pyrifolia)

Yoshihiro Takemura, Fumio Tamura
2018 Data in Brief  
Data on the draft genome obtained in this study has been deposited to the DNA Data Bank of Japan (DDBJ).  ...  The Japanese pear (Pyrus pyrifolia), a member of the family Rosaceae, is one of the most important fruit trees in Japan.  ...  Supporting information Transparency data associated with this article can be found in the online version at https://doi.org/ 10.1016/j.dib.2018.07.007.  ... 
doi:10.1016/j.dib.2018.07.007 pmid:30229099 pmcid:PMC6141501 fatcat:4phfb47f4jctzg65lek2wx4liq

Publicly-funded biobanks and networks in East Asia

Sunhee Lee, Paul Eunil Jung, Yeonhee Lee
2016 SpringerPlus  
Asian countries, especially China, Japan, and Korea are very active in biobanking activities under the strategic plans coordinated by their governments.  ...  With the enactment of the Nagoya Protocol, international competitions to secure biological resources are intensifying.  ...  Acknowledgements This study is supported by the Ministry of Science, ICT, and Future Planning and the National Research Foundation of Korea (NRF-2015M3A9B8028468).  ... 
doi:10.1186/s40064-016-2723-2 pmid:27462528 pmcid:PMC4945521 fatcat:oz4nqjgjazb5jczqptqstpahpa
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