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Improvements to services at the European Nucleotide Archive

Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad (+17 others)
2009 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www .ebi.ac.uk/ena) is Europe's primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide  ...  In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services.  ...  nucleotide sequence archive.  ... 
doi:10.1093/nar/gkp998 pmid:19906712 pmcid:PMC2808951 fatcat:7hx2okpxtbdcvpeoabj2q5emhe

The European Nucleotide Archive

R. Leinonen, R. Akhtar, E. Birney, L. Bower, A. Cerdeno-Tarraga, Y. Cheng, I. Cleland, N. Faruque, N. Goodgame, R. Gibson, G. Hoad, M. Jang (+9 others)
2010 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www .ebi.ac.uk/ena) is Europe's primary nucleotidesequence repository.  ...  The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services.  ...  THE EUROPEAN NUCLEOTIDE ARCHIVE The European Nucleotide Archive (ENA) operates as a public archive for nucleotide sequence data.  ... 
doi:10.1093/nar/gkq967 pmid:20972220 pmcid:PMC3013801 fatcat:pla5imfirvedhhclz3qcbuvgge

The European Nucleotide Archive in 2019

2019 Nucleic Acids Research  
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory's European Bioinformatics Institute provides open and freely available data deposition and  ...  access services across the spectrum of nucleotide sequence data types.  ...  have led to a broad range of nucleotide sequences that build the content of today's European Nucleotide Archive (ENA).  ... 
doi:10.1093/nar/gkz1063 pmid:31722421 pmcid:PMC7145635 fatcat:aorxf6izbvbkhb7jwbjawugaci

Petabyte-scale innovations at the European Nucleotide Archive

G. Cochrane, R. Akhtar, J. Bonfield, L. Bower, F. Demiralp, N. Faruque, R. Gibson, G. Hoad, T. Hubbard, C. Hunter, M. Jang, S. Juhos (+15 others)
2009 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis  ...  Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets.  ...  The European Nucleotide Archive (ENA), the collective name for nucleotide sequencing information archiving and presentation services at EMBL-EBI, comprising the EMBL Nucleotide Sequence Database and the  ... 
doi:10.1093/nar/gkn765 pmid:18978013 pmcid:PMC2686451 fatcat:xzwl3cvkjnarxbbbowzbnhazpi

Major submissions tool developments at the European nucleotide archive

C. Amid, E. Birney, L. Bower, A. Cerdeno-Tarraga, Y. Cheng, I. Cleland, N. Faruque, R. Gibson, N. Goodgame, C. Hunter, M. Jang, R. Leinonen (+15 others)
2011 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www .ebi.ac.uk/ena), Europe's primary nucleotide sequence resource, captures and presents globally comprehensive nucleic acid sequence and associated information  ...  During 2011, we have continued to operate and extend the broad range of ENA services.  ...  INTRODUCTION The European Nucleotide Archive (ENA) is maintained and developed at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and serves as Europe's primary  ... 
doi:10.1093/nar/gkr946 pmid:22080548 pmcid:PMC3245037 fatcat:qxbkwotuvfglhgef5ajiqczieq

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

The European Nucleotide Archive in 2018

Peter W Harrison, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Sam Holt, Abdulrahman Hussein, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu (+12 others)
2018 Nucleic Acids Research  
The European Nucleotide Archive (ENA; https://www. ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting  ...  this important resource to the scientific community to support and accelerate the global research effort.  ...  INTRODUCTION For over a third of a century, the European Nucleotide Archive (ENA) has served as a cornerstone of the world's bioinformatics infrastructure.  ... 
doi:10.1093/nar/gky1078 pmid:30395270 fatcat:kmr4vyojundfzabhv3dwdciamu

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  
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.  ...  This database content is shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence  ...  We are also thankful to Mari  ... 
doi:10.1093/nar/gkt1066 pmid:24194602 pmcid:PMC3964987 fatcat:vc62xknuzret3iehrzgxhzqhve

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

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Osamu Ogasawara
2018 Nucleic Acids Research  
The DDBJ Center collects nucleotide sequence data and associated biological information from researchers and also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database  ...  ), which is a member of the International Nucleotide Sequence Database Collaboration (INSDC) with the US National Center for Biotechnology Information and the European Bioinformatics Institute.  ...  We are thankful to Minae Kawashima, Licht Toyo-oka and Nobutaka Mitsuhashi of the NBDC as collaborators of the JGA project; Takatomo Fujisawa for validator development; Eli Kaminuma for the DDBJ Read Annotation  ... 
doi:10.1093/nar/gky1002 pmid:30357349 pmcid:PMC6323915 fatcat:3bgfc6a3lvf6fjavejrvwixzne

Assembly information services in the European Nucleotide Archive

Nima Pakseresht, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li (+18 others)
2013 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www. ebi.ac.uk/ena) is a repository for the world public domain nucleotide sequence data output.  ...  This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many enhancements have already been made available over the year to  ...  INTRODUCTION The European Nucleotide Archive (ENA) is the European resource in which the world's public domain sequencing data are maintained.  ... 
doi:10.1093/nar/gkt1082 pmid:24214989 pmcid:PMC3965037 fatcat:sddhoeztgfdkhbyx3zrms3ajza

The European Bioinformatics Institute in 2017: data coordination and integration

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
2017 Nucleic Acids Research  
This update gives a birds-eye view of EMBL-EBI's approach to data integration and service development as genomics begins to enter the clinic.  ...  The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https  ...  ChEBI (3), ChEMBL (4), the European Genome-phenome Archive (EGA) (5), the European Nucleotide Archive (ENA) (6), Ensembl (7), Ensembl Genomes (8), Europe PMC (9), IntAct (as part of the IMEx Consortium  ... 
doi:10.1093/nar/gkx1154 pmid:29186510 pmcid:PMC5753251 fatcat:ubzlegb2kjcltbtdftwsh6mlja

The International Nucleotide Sequence Database Collaboration

I. Karsch-Mizrachi, Y. Nakamura, G. Cochrane
2011 Nucleic Acids Research  
Among the many developments to INSDC resources in 2011 are the newly launched BioProject database and improved handling of assembly information.  ...  The members of the International Nucleotide Sequence Database Collaboration (INSDC; http:// www.insdc.org) set out to capture, preserve and present globally comprehensive public domain nucleotide sequence  ...  FUNDING NCBI by the Intramural Research Program of the National Institutes of Health; National Library of Medicine; European Nucleotide Archive by the European Molecular Biology Laboratory, the Wellcome  ... 
doi:10.1093/nar/gkr1006 pmid:22080546 pmcid:PMC3244996 fatcat:faxql3jvijaqxdfgdqoplvsh5e

Updates to BioSamples database at European Bioinformatics Institute

Adam Faulconbridge, Tony Burdett, Marco Brandizi, Mikhail Gostev, Rui Pereira, Drashtti Vasant, Ugis Sarkans, Alvis Brazma, Helen Parkinson
2013 Nucleic Acids Research  
accessioning at the point of submission to the European Nucleotide Archive and European Genotype Phenotype Archives and improved query response times.  ...  The BioSamples database at the EBI (http://www. ebi.ac.uk/biosamples) provides an integration point for BioSamples information between technology specific databases at the EBI, projects such as ENCODE  ...  We thank our colleagues Melissa Haendel and Chris Mungall for assistance with the Uberon SLIM generation and Segolene Ayme and Ana Rath of Orphanet.  ... 
doi:10.1093/nar/gkt1081 pmid:24265224 pmcid:PMC3965081 fatcat:lcjgrx5xy5bt5giyidtr2sammq

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  
This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.  ...  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.  ...  We are thankful to Mari T.  ... 
doi:10.1093/nar/gkv1105 pmid:26578571 pmcid:PMC4702806 fatcat:dsvzn2iivjb7jhqnqhoehswhtu

DDBJ progress report

E. Kaminuma, T. Kosuge, Y. Kodama, H. Aono, J. Mashima, T. Gojobori, H. Sugawara, O. Ogasawara, T. Takagi, K. Okubo, Y. Nakamura
2010 Nucleic Acids Research  
Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based  ...  The DNA Data Bank of Japan (DDBJ, http://www .ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis  ...  In particular, we thank Takako Mochizuki, Dr Hideki Nagasaki, Dr Toshihisa Okido and Dr Satoshi Saruhashi for consultations on the DRA and the pipeline and Professor Yoshio Tateno for support in the form  ... 
doi:10.1093/nar/gkq1041 pmid:21062814 pmcid:PMC3013661 fatcat:hqwqikzxbrhpvgsfc5fkecfzsy
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