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DDBJ in collaboration with mass-sequencing teams on annotation

Y. Tateno
2004 Nucleic Acids Research  
We are also in collaboration with a RIKEN team to accept and release the CAGE (Cap Analysis Gene Expression) data under a new category, MGA (Mass Sequences for Genome Annotation).  ...  On the other hand, we hosted workshops for human full-length cDNA annotation and participated in jamborees of mouse full-length cDNA annotation. The annotated data are made public at DDBJ.  ...  With this in mind, a RIKEN team sequenced a huge number of expressed sequences in 5 0 UTR, CAGE (Cap Analysis Gene Expression) sequences, for mouse (10) and plans to submit the data to DDBJ.  ... 
doi:10.1093/nar/gki020 pmid:15608189 pmcid:PMC539974 fatcat:jfo44562jbddrdhwtoaqdzpeh4

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

Y. Tateno
2002 Nucleic Acids Research  
HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. Both GIB and HGS have been updated incorporating newly available data and retrieval tools.  ...  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

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  
Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC).  ...  The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation.  ...  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

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 addition to the data collection, we have indexed the submitted data to the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org) to classify the entries into research  ...  ACKNOWLEDGEMENTS DDBJ is funded by Ministry of Education, Culture, Sports, Science and Technology (MEXT) with Management expenses grants for national university corporations.  ... 
doi:10.1093/nar/gkj111 pmid:16381940 pmcid:PMC1347473 fatcat:jxv72j4gebbi3ergixnyizrlqy

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  
We are collecting nucleotide sequence data and associated biological information from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with  ...  The DDBJ Center also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database Center to collect genotype and phenotype data of human individuals.  ...  We have semantically represented the DDBJ annotated sequence records into the Resource Description Framework (RDF) in collaboration with the Database Center for Life Science (DBCLS) (1, 26, 27) .  ... 
doi:10.1093/nar/gkx926 pmid:29040613 pmcid:PMC5753283 fatcat:3n45p6fz6bcfzgtv6j2prd44vq

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  
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  ...  The DNA Data Bank of Japan (DDBJ) (http://www. ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987).  ...  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

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  
In this period, we started a novel user announcement service using Really Simple Syndication (RSS) to deliver a list of data released from DDBJ on a daily basis.  ...  Concurrently, for read data registered in DRA, a semi-automatic annotation tool called the 'DDBJ Read Annotation Pipeline' was released as a preliminary step.  ...  Yoshio Tateno for support in the form of database maintenance and INSD collaboration.  ... 
doi:10.1093/nar/gkp847 pmid:19850725 pmcid:PMC2808917 fatcat:2yd7lgivcjdunjkd66kshsexim

DNA Data Bank of Japan at work on genome sequence data

Y Tateno
1998 Nucleic Acids Research  
We also developed a mass submission tool to cope with a large quantity of data. In addition, to provide genome data on WWW, we developed a genome information system using Java.  ...  Since the quantity of data is very large, we organized teams to conduct preliminary discussions with project teams about data submission and handling for release to the public.  ...  The sequence data were annotated in collaboration between the genome team and DDBJ (19) . The US team, however, went a bit farther in completing the whole genome (13) .  ... 
doi:10.1093/nar/26.1.16 pmid:9399792 pmcid:PMC147185 fatcat:5gln47g55fhudcoqzobyalkequ

Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration

Hallam Stevens
2017 Journal of the History of Biology  
This paper describes the origins of the International Nucleotide Sequence Database Collaboration between GenBank in the United States, the European Molecular Biology Laboratory Databank, and the DNA Database  ...  However, the large-scale international circulation of nucleotide sequence information did not begin with the Human Genome Project.  ...  At the NIG, I received the generous help of Machiko Itoh, who provided many documents related to DDBJ, and also helped me to organize interviews with those involved with  ... 
doi:10.1007/s10739-017-9490-y pmid:28986915 fatcat:panniideznbnhfelfspeygb6v4

The EMBL nucleotide sequence database

G Stoesser
1998 Nucleic Acids Research  
In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute.  ...  Database releases are produced quarterly and are distributed on CD-ROM.  ...  This sequence based taxonomy was created and is maintained by the NCBI with assistance from external advisors and in collaboration with EMBL and DDBJ.  ... 
doi:10.1093/nar/26.1.8 pmid:9399791 pmcid:PMC147241 fatcat:cnhmybcgfndazn73wbcr7tleu4

GENETICS: GenBank--Natural History in the 21st Century?

B. J. Strasser
2008 Science  
First, it instituted a tight collaboration with the EMBL database, established a few months earlier at Heidelberg, and, after 1986, with the DDBJ.  ...  The collaborations among GenBank, EMBL, and DDBJ required delicate negotiations to establish common entry standards; database managers could not rely on an equivalent of Linnaeus's binomial system, which  ... 
doi:10.1126/science.1163399 pmid:18948528 fatcat:y2g23bpdafbibhdngfrptwblgi

The Universal Protein Resource (UniProt)

2007 Nucleic Acids Research  
The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation.  ...  The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB).  ...  Additional support for the EBI's involvement in UniProt comes from the European Commission contract FELICS (021902RII3) and from the NIH grant 2 P41 HG002273-07.  ... 
doi:10.1093/nar/gkl929 pmid:17142230 pmcid:PMC1669721 fatcat:3doko4bysfhmzddimueyp2tj3y

The GenBank Sequence Database [chapter]

B. F. Francis Ouellette
2006 Methods of biochemical analysis  
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucl. Acids Res. 28, 24– 26. APPENDICES Appendix 3.1.  ...  One common type of annotation on a DNA sequence record is the coding sequence (CDS).  ... 
doi:10.1002/9780470110607.ch2 fatcat:uzsbdzxzhzcxlpc7pgvjhkoplq

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

James Rodney Brister, Yiming Bao, Carla Kuiken, Elliot J. Lefkowitz, Philippe Le Mercier, Raphael Leplae, Ramana Madupu, Richard H. Scheuermann, Seth Schobel, Donald Seto, Susmita Shrivastava, Peter Sterk (+3 others)
2010 Viruses  
Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology.  ...  sequence databases.  ...  Craig Venter Institute for sponsoring the Genome Annotation Workshop.  ... 
doi:10.3390/v2102258 pmid:21994619 pmcid:PMC3185566 fatcat:twb65cwuu5htfccxzaft2nr5gu
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