Literature DB >> 25404130

Content discovery and retrieval services at the European Nucleotide Archive.

Nicole Silvester1, Blaise Alako2, Clara Amid2, Ana Cerdeño-Tárraga2, Iain Cleland2, Richard Gibson2, Neil Goodgame2, Petra Ten Hoopen2, Simon Kay2, Rasko Leinonen2, Weizhong Li2, Xin Liu2, Rodrigo Lopez2, Nima Pakseresht2, Swapna Pallreddy2, Sheila Plaister2, Rajesh Radhakrishnan2, Marc Rossello2, Alexander Senf2, Dmitriy Smirnov2, Ana Luisa Toribio2, Daniel Vaughan2, Vadim Zalunin2, Guy Cochrane2.   

Abstract

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its discoverability and usability. In response to this, ENA has been introducing and improving checklists for use during submission and expanding its search facilities to provide targeted search results. Here, we give a brief update on ENA content and some major developments undertaken in data submission services during 2014. We then describe in more detail the services we offer for data discovery and retrieval.
© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2014        PMID： 25404130      PMCID： PMC4383942          DOI： 10.1093/nar/gku1129

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  8 in total

1.  RNAcentral: A vision for an international database of RNA sequences.

Authors:  Alex Bateman; Shipra Agrawal; Ewan Birney; Elspeth A Bruford; Janusz M Bujnicki; Guy Cochrane; James R Cole; Marcel E Dinger; Anton J Enright; Paul P Gardner; Daniel Gautheret; Sam Griffiths-Jones; Jen Harrow; Javier Herrero; Ian H Holmes; Hsien-Da Huang; Krystyna A Kelly; Paul Kersey; Ana Kozomara; Todd M Lowe; Manja Marz; Simon Moxon; Kim D Pruitt; Tore Samuelsson; Peter F Stadler; Albert J Vilella; Jan-Hinnerk Vogel; Kelly P Williams; Mathew W Wright; Christian Zwieb
Journal:  RNA       Date:  2011-09-22       Impact factor: 4.942

2.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:  Pelin Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R Cole; Linda Amaral-Zettler; Jack A Gilbert; Ilene Karsch-Mizrachi; Anjanette Johnston; Guy Cochrane; Robert Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Philippe Rocca-Serra; Peter Sterk; Manimozhiyan Arumugam; Mark Bailey; Laura Baumgartner; Bruce W Birren; Martin J Blaser; Vivien Bonazzi; Tim Booth; Peer Bork; Frederic D Bushman; Pier Luigi Buttigieg; Patrick S G Chain; Emily Charlson; Elizabeth K Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed A Fuhrman; Rachel E Gallery; Dirk Gevers; Richard A Gibbs; Inigo San Gil; Antonio Gonzalez; Jeffrey I Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Andrew L Kau; Scott T Kelley; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L Lauber; Teresa Legg; Ruth E Ley; Catherine A Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A Methé; Folker Meyer; Brian Muegge; Sara Nakielny; Karen E Nelson; Diana Nemergut; Josh D Neufeld; Lindsay K Newbold; Anna E Oliver; Norman R Pace; Giriprakash Palanisamy; Jörg Peplies; Joseph Petrosino; Lita Proctor; Elmar Pruesse; Christian Quast; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A Relman; Susanna Assunta-Sansone; Patrick D Schloss; Lynn Schriml; Rohini Sinha; Michelle I Smith; Erica Sodergren; Aymé Spo; Jesse Stombaugh; James M Tiedje; Doyle V Ward; George M Weinstock; Doug Wendel; Owen White; Andrew Whiteley; Andreas Wilke; Jennifer R Wortman; Tanya Yatsunenko; Frank Oliver Glöckner
Journal:  Nat Biotechnol       Date:  2011-05       Impact factor: 54.908

3.  The complete genome sequence of a Neanderthal from the Altai Mountains.

Authors:  Kay Prüfer; Fernando Racimo; Nick Patterson; Flora Jay; Sriram Sankararaman; Susanna Sawyer; Anja Heinze; Gabriel Renaud; Peter H Sudmant; Cesare de Filippo; Heng Li; Swapan Mallick; Michael Dannemann; Qiaomei Fu; Martin Kircher; Martin Kuhlwilm; Michael Lachmann; Matthias Meyer; Matthias Ongyerth; Michael Siebauer; Christoph Theunert; Arti Tandon; Priya Moorjani; Joseph Pickrell; James C Mullikin; Samuel H Vohr; Richard E Green; Ines Hellmann; Philip L F Johnson; Hélène Blanche; Howard Cann; Jacob O Kitzman; Jay Shendure; Evan E Eichler; Ed S Lein; Trygve E Bakken; Liubov V Golovanova; Vladimir B Doronichev; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Nature       Date:  2013-12-18       Impact factor: 49.962

4.  RNAcentral: an international database of ncRNA sequences.

Authors:  Anton I Petrov; Simon J E Kay; Richard Gibson; Eugene Kulesha; Dan Staines; Elspeth A Bruford; Mathew W Wright; Sarah Burge; Robert D Finn; Paul J Kersey; Guy Cochrane; Alex Bateman; Sam Griffiths-Jones; Jennifer Harrow; Patricia P Chan; Todd M Lowe; Christian W Zwieb; Jacek Wower; Kelly P Williams; Corey M Hudson; Robin Gutell; Michael B Clark; Marcel Dinger; Xiu Cheng Quek; Janusz M Bujnicki; Nam-Hai Chua; Jun Liu; Huan Wang; Geir Skogerbø; Yi Zhao; Runsheng Chen; Weimin Zhu; James R Cole; Benli Chai; Hsien-Da Huang; His-Yuan Huang; J Michael Cherry; Artemis Hatzigeorgiou; Kim D Pruitt
Journal:  Nucleic Acids Res       Date:  2014-10-28       Impact factor: 16.971

5.  The International Nucleotide Sequence Database Collaboration.

Authors:  Yasukazu Nakamura; Guy Cochrane; Ilene Karsch-Mizrachi
Journal:  Nucleic Acids Res       Date:  2012-11-24       Impact factor: 16.971

6.  Updates to BioSamples database at European Bioinformatics Institute.

Authors:  Adam Faulconbridge; Tony Burdett; Marco Brandizi; Mikhail Gostev; Rui Pereira; Drashtti Vasant; Ugis Sarkans; Alvis Brazma; Helen Parkinson
Journal:  Nucleic Acids Res       Date:  2013-11-21       Impact factor: 16.971

7.  EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

Authors:  Sarah Hunter; Matthew Corbett; Hubert Denise; Matthew Fraser; Alejandra Gonzalez-Beltran; Christopher Hunter; Philip Jones; Rasko Leinonen; Craig McAnulla; Eamonn Maguire; John Maslen; Alex Mitchell; Gift Nuka; Arnaud Oisel; Sebastien Pesseat; Rajesh Radhakrishnan; Philippe Rocca-Serra; Maxim Scheremetjew; Peter Sterk; Daniel Vaughan; Guy Cochrane; Dawn Field; Susanna-Assunta Sansone
Journal:  Nucleic Acids Res       Date:  2013-10-27       Impact factor: 16.971

8.  Assembly information services in the European Nucleotide Archive.

Authors:  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; Xin Liu; Rodrigo Lopez; Hamish McWilliam; Arnaud Oisel; Swapna Pallreddy; Sheila Plaister; Rajesh Radhakrishnan; Stephane Rivière; Marc Rossello; Alexander Senf; Nicole Silvester; Dmitriy Smirnov; Silvano Squizzato; Petra ten Hoopen; Ana Luisa Toribio; Daniel Vaughan; Vadim Zalunin; Guy Cochrane
Journal:  Nucleic Acids Res       Date:  2013-11-08       Impact factor: 16.971
  8 in total
  28 in total

1.  Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

Authors:  Lars Barquist; Sarah W Burge; Paul P Gardner
Journal:  Curr Protoc Bioinformatics       Date:  2016-06-20

Review 2.  Proteogenomics from a bioinformatics angle: A growing field.

Authors:  Gerben Menschaert; David Fenyö
Journal:  Mass Spectrom Rev       Date:  2015-12-15       Impact factor: 10.946

3.  The EMBL-EBI bioinformatics web and programmatic tools framework.

Authors:  Weizhong Li; Andrew Cowley; Mahmut Uludag; Tamer Gur; Hamish McWilliam; Silvano Squizzato; Young Mi Park; Nicola Buso; Rodrigo Lopez
Journal:  Nucleic Acids Res       Date:  2015-04-06       Impact factor: 16.971

4.  The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.

Authors:  Silvano Squizzato; Young Mi Park; Nicola Buso; Tamer Gur; Andrew Cowley; Weizhong Li; Mahmut Uludag; Sangya Pundir; Jennifer A Cham; Hamish McWilliam; Rodrigo Lopez
Journal:  Nucleic Acids Res       Date:  2015-04-08       Impact factor: 16.971

5.  ATtRACT-a database of RNA-binding proteins and associated motifs.

Authors:  Girolamo Giudice; Fátima Sánchez-Cabo; Carlos Torroja; Enrique Lara-Pezzi
Journal:  Database (Oxford)       Date:  2016-04-07       Impact factor: 3.451

6.  PhytoPath: an integrative resource for plant pathogen genomics.

Authors:  Helder Pedro; Uma Maheswari; Martin Urban; Alistair George Irvine; Alayne Cuzick; Mark D McDowall; Daniel M Staines; Eugene Kulesha; Kim Elizabeth Hammond-Kosack; Paul Julian Kersey
Journal:  Nucleic Acids Res       Date:  2015-10-17       Impact factor: 16.971

7.  BacWGSTdb, a database for genotyping and source tracking bacterial pathogens.

Authors:  Zhi Ruan; Ye Feng
Journal:  Nucleic Acids Res       Date:  2015-10-03       Impact factor: 16.971

8.  The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Authors: 
Journal:  Nucleic Acids Res       Date:  2015-11-28       Impact factor: 16.971

9.  Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.

Authors:  David Bousfield; Johanna McEntyre; Sameer Velankar; George Papadatos; Alex Bateman; Guy Cochrane; Jee-Hyub Kim; Florian Graef; Vid Vartak; Blaise Alako; Niklas Blomberg
Journal:  F1000Res       Date:  2016-02-11

10.  DNA data bank of Japan (DDBJ) progress report.

Authors:  Jun Mashima; Yuichi Kodama; Takehide Kosuge; Takatomo Fujisawa; Toshiaki Katayama; Hideki Nagasaki; Yoshihiro Okuda; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Yasukazu Nakamura; Toshihisa Takagi
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971
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