Facing growth in the European Nucleotide Archive

Cochrane, Guy; Alako, Blaise T. F.; Amid, Clara; Bower, Lawrence; Cerdeño-Tárraga, Ana; Cleland, Ian; Gibson, Richard L.; Goodgame, Neil; Jang, Mikyung; Kay, Simon; Leinonen, Rasko; Lin, Xiao; López, Rodrigo; McWilliam, Hamish; Oisel, Arnaud; Pakseresht, Nima; Pallreddy, Swapna; Park, Young Mi; Plaister, Sheila; Radhakrishnan, Rajesh; Rivière, Stéphane; Rossello, Marc; Senf, Alexander; Silvester, Nicole C.; Smirnov, Dmitriy; Hoopen, Petra ten; Toribio, Ana Luisa; Vaughan, David; Zalunin, Vadim

doi:10.1093/nar/gks1175

Cited by 74 publications

(51 citation statements)

References 7 publications

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“…Individual data resources, such as ChEBI (4), ENA (5), Gene Expression Atlas (6) and UniProt (7), provide web interfaces and Web Services (Table 1) tailored to the specifics of their data and the usage patterns required by consumers of their data. These interfaces cater well for searches against the specific resource and address searches and data retrieval operations concerning data from the specific resource; however, this can prove to be an issue when access to multiple data sources is required because each data resource has to be handled separately.…”

Section: Web Servicesmentioning

confidence: 99%

Analysis Tool Web Services from the EMBL-EBI

McWilliam

Uludağ

et al. 2013

Nucleic Acids Research

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Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

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Section: Web Servicesmentioning

confidence: 99%

Analysis Tool Web Services from the EMBL-EBI

McWilliam

Uludağ

et al. 2013

Nucleic Acids Research

Self Cite

1,524

1,170

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“…In 2013, ENA published updates to the effect that the SRA had tripled in size since 2011 and was consistently doubling in size every ten months; it now comprised data from over 14,000 studies. Furthermore, comparable growth is expected for another five to ten years, even under modest predictions [51]. In addition to the SRA, ENA also has the Trace Archive and the EMBL-Bank.…”

Section: General Sequence Databasesmentioning

confidence: 87%

Bioinformatics: Concepts, Methods, and Data

Robinson

Afzal

Leader

2014

Handbook of Pharmacogenomics and Stratified Medicine

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“…Aside from UniProtKB and the PDB, amongst the strongest surviving databases are EMBL (now part of ENA (Cochrane et al, 2013)), GenBank (Benson et al, 2014), DDBJ (Kosuge et al, 2014), Ensembl (Flicek et al, 2014) and InterPro (Mitchell et al, 2014). Several of these will benefit from being part of ELIXIR, in which they are 'named services' that may ultimately qualify for core support, whether at the EBI or at designated ELIXIR Nodes across Europe as their host countries ratify ELIXIR's Consortium Agreement.…”

Section: Case Studiesmentioning

confidence: 99%

Longevity of Biological Databases

2015

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Public Web-based databases are essential for present-day biological research: they i) store the results of past laboratory experiments; ii) guide the focus of future ones; and, iii) allow all to benefit from the wealth of information they contain. Many new databases are born each year; but how long do they live? This study looked at the 18-year survival of 326 databases. Over 60% were dead within that time period, and a further 14% were archived, no longer updated. Those that survived were, for the most part, important to their institution's main focus, and had core institutional support. Database longevity depends on the existence of infrastructures that are underpinned by long-term financial strategies. Researchers and funders need to consider the ramifications for the security of their data, and of the financial investments in them, if they choose to create new databases independently of core infrastructures.

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Facing growth in the European Nucleotide Archive

Cited by 74 publications

References 7 publications

Analysis Tool Web Services from the EMBL-EBI

Analysis Tool Web Services from the EMBL-EBI

Bioinformatics: Concepts, Methods, and Data

Longevity of Biological Databases

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