Ensembl variation resources

BMC Genomics

Database

Daniel Rios¹  Damian Smedley¹  Ewan Birney¹  Fiona Cunningham¹  Yuan Chen¹  William M McLaren¹  Giulietta M Spudich¹  Eugene Kulesha¹  Paul Flicek²  Simon Brent³  James Smith³  Pablo Marin-Garcia³  Bethan Pritchard³ 

[1] European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA, Hinxton, Cambridge, UK;Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA, Hinxton, Cambridge, UK;

关键词: Variation Data;    Application Program Interface;    High Linkage Disequilibrium;    National Human Genome Research Institute;    Ensembl Variation;   

DOI  :  10.1186/1471-2164-11-293

 received in 2009-09-10, accepted in 2010-05-11,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics.DescriptionThe Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl.ConclusionsVariation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

【 授权许可】

Unknown   
© Chen et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.