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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 are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from  ...  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

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  
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.  ...  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.  ...  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 (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

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

DDBJ Database updates and computational infrastructure enhancement

2019 Nucleic Acids Research  
In order to accommodate the rapidly growing amount of deoxyribonucleic acid (DNA) nucleotide sequence data, NIG replaced its supercomputer system, which is designed for big data analysis of genome data  ...  The NIG operates the NIG supercomputer as a computational basis for the construction of DDBJ databases and as a large-scale computational resource for Japanese biologists and medical researchers.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Naofumi Ishikawa and all members of Bioinformation and DDBJ Center for their assistance in data collection, annotation, release  ... 
doi:10.1093/nar/gkz982 pmid:31724722 pmcid:PMC7145692 fatcat:uubxnpbeqvabrkkaw5ah4q7hzm

DDBJ in preparation for overview of research activities behind data submissions

K. Okubo
2006 Nucleic Acids Research  
The results of indexing also allow one to grasp research projects in life sciences that promoted and produced the DNA sequences submitted to INSDC.  ...  In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 956 826 entries or 1 741 313 111 bases.  ...  Funding to pay the Open Access publication charges for this article was provided by Japan Society for the Promotion of Science Grant# 16255006.  ... 
doi:10.1093/nar/gkj111 pmid:16381940 pmcid:PMC1347473 fatcat:jxv72j4gebbi3ergixnyizrlqy

DDBJ dealing with mass data produced by the second generation sequencer

H. Sugawara, K. Ikeo, S. Fukuchi, T. Gojobori, Y. Tateno
2009 Nucleic Acids Research  
DNA Data Bank of Japan (DDBJ) (http://www.ddbj. nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008.  ...  The releases in this period include genome scale data of Bombyx mori, Oryzas latipes, Drosophila and Lotus japonicus.  ...  ACKNOWLEDGEMENTS We thank all staff of DDBJ for the data collection, annotation, release, management and software development.  ... 
doi:10.1093/nar/gkn724 pmid:18927114 pmcid:PMC2686496 fatcat:ii3mg3fi5jhnnpxoym7xz76fjy

DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Osamu Ogasawara
2018 Nucleic Acids Research  
The Genomic Expression Archive (GEA) for functional genomics data from microarray and high-throughput sequencing experiments has been established at the DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp  ...  The DDBJ Center also operates the NIG supercomputer, prepared for analyzing large-scale genome sequences. We now offer a secure platform specifically to handle personal human genomes.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge Koji Watanabe, Naofumi Ishikawa, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi, Masanori Arita and all members of the DDBJ Center for their support in data  ... 
doi:10.1093/nar/gky1002 pmid:30357349 pmcid:PMC6323915 fatcat:3bgfc6a3lvf6fjavejrvwixzne

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2014 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 to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Takeshi Tsurusawa, Koji Watanabe, Chiharu Kawagoe and all members of the DDBJ Center for their assistance in data collection, annotation, release  ... 
doi:10.1093/nar/gku1120 pmid:25477381 pmcid:PMC4383935 fatcat:tcpa3elm3zglbo5lauuatx3nca

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

Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2009 Nucleic Acids Research  
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 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  ...  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/gkp847 pmid:19850725 pmcid:PMC2808917 fatcat:2yd7lgivcjdunjkd66kshsexim

DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences

Eli Kaminuma, Yukino Baba, Masahiro Mochizuki, Hirotaka Matsumoto, Haruka Ozaki, Toshitsugu Okayama, Takuya Kato, Shinya Oki, Takatomo Fujisawa, Yasukazu Nakamura, Masanori Arita, Osamu Ogasawara (+2 others)
2020 Genes & Genetic Systems  
In this report, we describe how we investigated the potential of crowdsourced modelling for a life science task by conducting a machine learning competition, the DNA Data Bank of Japan (DDBJ) Data Analysis  ...  However, finding research collaborators with knowledge of machine learning techniques is difficult for many experimental life scientists.  ...  This research was partially supported by management expenses grants from the DNA Data Bank of Japan, the ROIS, and JST CREST Grant Number JPMJCR1501, Japan.  ... 
doi:10.1266/ggs.19-00034 pmid:32213716 fatcat:ae6ecvdeo5bzrnddbrwpjs3b6u

DDBJ progress report: a new submission system for leading to a correct annotation

Takehide Kosuge, Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2013 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.  ...  JGA permanently archives and shares all types of individual human genetic and phenotypic data. We also introduce improvements in the DDBJ services and databases made during the past year.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Takeshi Tsurusawa, Keiichi Nagai and all members of DDBJ for their assistance in data collection, annotation, release and software development.  ... 
doi:10.1093/nar/gkt1066 pmid:24194602 pmcid:PMC3964987 fatcat:vc62xknuzret3iehrzgxhzqhve

Introduction on Several Popular Nucleic Acids Databases

Changmin Liao
2013 Journal of Computer Engineering and Informatics  
Sequence Database), GenBank, DDBJ (DNA Data Bank of Japan), GDB (Human Genome Database), EID (Exon-Intron Dabase), EPD (Eukaryotic Promoter Data) and RNAiDB (RNA Interference Database).  ...  Nucleic acids are major biological molecules essential for life, and everyday, there are large number of nucleic acids sequences that are released and searched.  ...  Xiaohong Liu (College of Life Science, China West Normal University, P. R. China) for his critical reading to my manuscript.  ... 
doi:10.5963/jcei0102005 fatcat:3uwyh5eakbdfriznaeuv2jnsdi

Archiving next generation sequencing data

Martin Shumway, Guy Cochrane, Hideaki Sugawara
2009 Nucleic Acids Research  
the DNA Data Bank of Japan (DDBJ), have established the Sequence Read Archive (SRA) to provide the scientific community with an archival destination for next generation data sets.  ...  Users of these resources can obtain data sets deposited in any of the three SRA instances. Links and submission instructions are provided.  ...  Data Bank of Japan (DDBJ).  ... 
doi:10.1093/nar/gkp1078 pmid:19965774 pmcid:PMC2808927 fatcat:zhs53qq7pbdcbgc4oxwkxuwxqe
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