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Facing growth in the European Nucleotide Archive

Guy Cochrane, Blaise Alako, Clara Amid, Lawrence Bower, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Mikyung Jang, Simon Kay, Rasko Leinonen, Xiu Lin (+17 others)
2012 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www. ebi.ac.uk/ena/) collects, maintains and presents comprehensive nucleic acid sequence and related information as part of the permanent public scientific  ...  Here, we provide brief updates on ENA content developments and major service enhancements in 2012 and describe in more detail two important areas of development and policy that are driven by ongoing growth  ...  INTRODUCTION The European Nucleotide Archive (ENA; http://www.ebi. ac.uk/ena) has for the last 30 years captured, organized and presented the world's public domain output of sequence information.  ... 
doi:10.1093/nar/gks1175 pmid:23203883 pmcid:PMC3531187 fatcat:fdf5xomwnbdz3kiv3ngyh44dty

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  ...  Covering the spectrum from raw data to assembled and functionally annotated genomes, the ENA has witnessed a dramatic growth resulting from advances in sequencing technology and ever broadening application  ...  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

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.  ...  ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets.  ...  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 2016: Data growth and integration

Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler
2015 Nucleic Acids Research  
In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep  ...  Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework  ...  ACKNOWLEDGEMENTS EMBL-EBI is indebted to its funders, including the EMBL member states, the European Commission, the Wellcome Trust, the UK Research Councils, the US National Institutes of Health, our  ... 
doi:10.1093/nar/gkv1352 pmid:26673705 pmcid:PMC4702932 fatcat:2oonfh72mrbpfi2ywith6updti

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences

2019 Nucleic Acids Research  
Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world.  ...  Training is a core mission of EMBL-EBI and in 2018 our training team served more users, both in-person and through web-based programmes, than ever before.  ...  ACKNOWLEDGEMENTS We were able to continue to scale our infrastructure and meet demand thanks in part to support from the UK's Large Facilities Capital Fund (LFCF).  ... 
doi:10.1093/nar/gkz1033 pmid:31701143 pmcid:PMC6943058 fatcat:i2gcxbfkprb37etd37stq4t74a

The European Nucleotide Archive in 2017

Nicole Silvester, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Peter W Harrison, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu (+11 others)
2017 Nucleic Acids Research  
For 35 years the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) has been responsible for making the world's public sequencing data available to the scientific community.  ...  Advances in sequencing technology have driven exponential growth in the volume of data to be processed and stored and a substantial broadening of the user community.  ...  European Nucleotide Archive (ENA), maintained at the EMBL European Bioinformatics Institute (EMBL-EBI).  ... 
doi:10.1093/nar/gkx1125 pmid:29140475 pmcid:PMC5753375 fatcat:s2q7ka7s5nbufi7gnztodzyzym

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database

G. Cochrane, R. Akhtar, P. Aldebert, N. Althorpe, A. Baldwin, K. Bates, S. Bhattacharyya, J. Bonfield, L. Bower, P. Browne, M. Castro, T. Cox (+24 others)
2007 Nucleic Acids Research  
In the face of increasing requirements for nucleotide trace, sequence and annotation data archiving, data capture priority decisions have been taken at the European Nucleotide Archive.  ...  The Ensembl Trace Archive (http://trace.ensembl. org/) and the EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), known together as the European Nucleotide Archive, continue to see growth  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by EMBL. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm1018 pmid:18039715 pmcid:PMC2238915 fatcat:eergvcffqvfsdkawezyg4fwqii

The European Bioinformatics Institute's data resources 2014

Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet Thornton
2013 Nucleic Acids Research  
Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of  ...  ACKNOWLEDGEMENTS The EMBL-EBI is indebted to the support of its funders: EMBL's member states, the European Commission, the Wellcome Trust, the UK Research Councils, the US National Institutes of Health  ...  The authors would like to thank the many colleagues who provided input to this manuscript.  ... 
doi:10.1093/nar/gkt1206 pmid:24271396 pmcid:PMC3964968 fatcat:7dgar73rqjhwzci6shbolfpvfq

E-BioSci, digital archives, databases, and the changing face of publishing

Les Grivell
2001 Serials: The Journal for the Serials Community  
Les Grivell The changing face of publishing 183 E-BioSci is the European Molecular Biology Organisation's initiative in e-publishing.  ...  To do this, it is necessary to describe how such changes are being driven by quantum leaps in technology (both in information science and biology), by the growth of new disciplines, including genomics  ...  EMBL Nucleotide Sequence Database.  ... 
doi:10.1629/14183 fatcat:xulkx4jl35az5i2zo7xcx5gjsm

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

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data

Robert Petryszak, Nuno A Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y Amy Tang, Alvis Brazma, Bonnie Berger
2017 Bioinformatics  
future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer.  ...  Motivation: The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those  ...  the Ensembl and WormBase ParaSite teams for facilitating timely access to the genome references; the ENA Team for their assistance in retrieval the raw RNA-Seq data; and finally to the Samples, Phenotypes  ... 
doi:10.1093/bioinformatics/btx143 pmid:28369191 pmcid:PMC5870697 fatcat:ild6vn5ll5hcfj4alj5kksj234

The European Bioinformatics Institute in 2018: tools, infrastructure and training

Charles E Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler
2018 Nucleic Acids Research  
The European Bioinformatics Institute (https://www.ebi.ac.uk/) archives, curates and analyses life sciences data produced by researchers throughout the world, and makes these data available for re-use  ...  pdbe-kb), which collates functional annotations and predictions for structure data in the Protein Data Bank.  ...  ACKNOWLEDGEMENTS EMBL-EBI is indebted to its funders, including the EMBL member states, the European Commission, Wellcome, the UK Research Councils, the US National Institutes of Health, our Industry Programme  ... 
doi:10.1093/nar/gky1124 pmid:30445657 pmcid:PMC6323906 fatcat:ww5xqc5aorgone5pt43p43o6tu

Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and Encephalopathy

Eugen Domann, Florence Fischer, Fabian Glowatzki, Moritz Fritzenwanker, Torsten Hain, Silke Zechel-Gran, Susanne Giffhorn-Katz, Bernd A. Neubauer
2016 Genome Announcements  
Here, we report the draft genome sequence of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel syndrome and previous d -lactic acidosis/encephalopathy.  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ...  FUNDING INFORMATION This work was funded by the German Ministry of Education and Research (BMBF) as part of the research consortium ANTHONIA (grant no. 0315379A to E.D.).  ... 
doi:10.1128/genomea.00747-16 pmid:27469967 pmcid:PMC4966471 fatcat:ssp5hxqzlref3bnkncynimkx2a

Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective [chapter]

T.K. Attwood, A. Gisel, N-E. Eriksson, E. Bongcam-Rudloff
2011 Bioinformatics - Trends and Methodologies  
Building on the ongoing sequencing work, this advance set the scene for an exciting new era in which structure determination took centre stage in our quest to understand the biophysical mechanisms that  ...  In the decade that followed, time-consuming manual processes were gradually superseded with the advent of automated peptide sequencers, which increased the rate of sequence determination considerably.  ...  Together, EMBL-Bank and the ETA became known as ENA, the European Nucleotide Archive, Europe's primary nucleotide-sequence repository (Cochrane et al., 2008) .  ... 
doi:10.5772/23535 fatcat:dwe4umftd5anrfobkciktbmg3m

Biobanking with Big Data: A Need for Developing "Big Data Metrics"

Kozlakidis Zisis
2016 Biopreservation and Biobanking  
The European Nucleotide Archive (ENA) provides a useful example, where the experience of the last 30 years has resulted in three tiers of data, divided simply into unprocessed, processed, and interpreted  ...  , and the European Statistical System, 2003) .  ... 
doi:10.1089/bio.2015.0106 pmid:27249183 fatcat:egb56ln72zbf7fphctodmeqmsy
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