Ensembl 2014.
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ABSTRACT:
SUBMITTER: Flicek P
PROVIDER: S-EPMC3964975 | biostudies-literature | 2014 Jan
REPOSITORIES: biostudies-literature
Publications
Ensembl 2014.
Flicek Paul P Amode M Ridwan MR Barrell Daniel D Beal Kathryn K Billis Konstantinos K Brent Simon S Carvalho-Silva Denise D Clapham Peter P Coates Guy G Fitzgerald Stephen S Gil Laurent L Girón Carlos García CG Gordon Leo L Hourlier Thibaut T Hunt Sarah S Johnson Nathan N Juettemann Thomas T Kähäri Andreas K AK Keenan Stephen S Kulesha Eugene E Martin Fergal J FJ Maurel Thomas T McLaren William M WM Murphy Daniel N DN Nag Rishi R Overduin Bert B Pignatelli Miguel M Pritchard Bethan B Pritchard Emily E Riat Harpreet S HS Ruffier Magali M Sheppard Daniel D Taylor Kieron K Thormann Anja A Trevanion Stephen J SJ Vullo Alessandro A Wilder Steven P SP Wilson Mark M Zadissa Amonida A Aken Bronwen L BL Birney Ewan E Cunningham Fiona F Harrow Jennifer J Herrero Javier J Hubbard Tim J P TJ Kinsella Rhoda R Muffato Matthieu M Parker Anne A Spudich Giulietta G Yates Andy A Yates Andy A Zerbino Daniel R DR Searle Stephen M J SM
Nucleic acids research 20131206 Database issue
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of ...[more]
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Project description:MotivationWe present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language.Availability and implementationThe Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest.
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Project description:Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.
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Project description:The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
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