Ensembl 2014

Paul Flicek,Javier Herrero,Ewan Birney,Anne Parker,Jennifer Harrow,Rhoda Kinsella,Peter Clapham,Amonida Zadissa,Stephen Fitzgerald,Daniel N Murphy,Stephen Keenan,Eugene Kulesha,Simon Brent,Sarah Hunt,Kieron Taylor,Laurent Gil,Fiona Cunningham,Stephen J Trevanion,Rishi Nag,Fergal J Martin,Giulietta Spudich,Thomas Juettemann,Matthieu Muffato,Bethan Pritchard,Miguel Pignatelli,Thomas Maurel,Mark Wilson,Magali Ruffier,Alessandro Vullo,Carlos García Girón,Denise Carvalho-Silva,Emily Pritchard,Daniel Barrell,Kathryn Beal,Bert Overduin,Thibaut Hourlier,Guy Coates,Anja Thormann,Andy Yates,Daniel R Zerbino,Konstantinos Billis,Nathan Johnson,Steven P Wilder,Bronwen Aken ,Tim Hubbard ,William Mclaren ,Leo I Gordon ,Harpreet Singh Riat ,Dan Sheppard ,Andreas Kähäri ,M Ridwan Amode ,Stephen M J Searle

doi:10.1093/nar/gkt1196

Ensembl 2014

Paul Flicek, Javier Herrero + Show 50 more

Open Access

https://doi.org/10.1093/nar/gkt1196

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Abstract

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 new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.

Highlights

The Ensembl project creates and distributes genome annotations and provides integrated views of other valuable genomic data for supported chordate genomes
Ensembl provides unique tools, datasets and user support compared to similar projects such as the UCSC Genome Browser [1], while supporting community standards that promote interoperability in genomics
We have developed and distribute an extensive, open software infrastructure with diverse analysis pipelines supporting a variety of genome analyses [2] and the artificial intelligence inspired eHive analysis management system [3]; data mining and analysis tools that include BioMart [4] and the Ensembl Variant Effect Predictor (VEP) [5]; supported and robust application programing interfaces (APIs) [6] and a unique genome browser interface [7]

Summary

Introduction

The Ensembl project (http://www.ensembl.org) creates and distributes genome annotations and provides integrated views of other valuable genomic data for supported chordate genomes. Ensembl provides unique tools, datasets and user support compared to similar projects such as the UCSC Genome Browser [1], while supporting community standards that promote interoperability in genomics.

Results

Conclusion