Ensembl variation resources.
Ensembl variation resources.
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DOI：
10.1186/1471-2164-11-293
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发表时间：
2010-05-11
期刊：
影响因子：
4.4
通讯作者：
Flicek P
中科院分区：
文献类型：
--
作者：
Chen Y;Cunningham F;Rios D;McLaren WM;Smith J;Pritchard B;Spudich GM;Brent S;Kulesha E;Marin-Garcia P;Smedley D;Birney E;Flicek P
成熟的基因组学领域正在迅速增加已测序基因组的数量，并从先前测序的基因组中产生更多信息。这些额外的信息大多是来自于对一个给定物种的多个个体进行采样的变异数据，目的是发现新的变异，并描述已知变异的种群频率。这些数据对许多研究具有巨大的价值，包括那些旨在理解进化和将基因型与表型联系起来的研究。为了最大限度地发挥数据的效用，需要以可访问的方式存储数据，从而促进变异数据与其他基因组资源（如基因注释和比较基因组学）的整合。Ensembl项目为各种各样的脊索动物基因组提供了全面和集成的变异资源。本文详细介绍了数据的来源和建立Ensembl变异数据库的方法。通过解释可用查询选项的范围（从使用交互式web显示到在线数据挖掘工具以及以编程方式直接连接到数据服务器），本文还探讨了信息的实用性。它很好地概述了变异资源和未来在Ensembl中扩展变异数据的计划。变异数据是理解个体间功能和表型差异的重要关键。新的测序和基因分型技术的发展极大地增加了几乎所有基因组已知的变异数据量。Ensembl变异资源被集成到Ensembl基因组浏览器中，并提供了一种在广泛使用的基因组生物信息学系统中访问这些数据的综合方法。所有的Ensembl数据都可以在http://www.ensembl.org和公共MySQL数据库服务器上免费获得。
The 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. The 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. Variation 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.