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DNA Data Bank of Japan (DDBJ) for genome scale research in life science
2002
Nucleic Acids Research
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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
2015
Nucleic Acids Research
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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
2003
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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
2017
Nucleic Acids Research
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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
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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
2006
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2020
Genes & Genetic Systems
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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
2013
Nucleic Acids Research
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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
2013
Journal of Computer Engineering and Informatics
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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
2009
Nucleic Acids Research
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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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