Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
复制标题
DOI：
10.1093/database/bax020
复制
发表时间：
2017-01-01
期刊：
影响因子：
--
通讯作者：
Flicek P
中科院分区：
文献类型：
--
作者：
Ruffier M;Kähäri A;Komorowska M;Keenan S;Laird M;Longden I;Proctor G;Searle S;Staines D;Taylor K;Vullo A;Yates A;Zerbino D;Flicek P
EnSembl软件资源是存储、访问和操作基因组组合及其功能注释的稳定基础设施。EnSembl‘Core’数据库和应用程序编程接口(API)是我们的第一个主要软件基础设施，并且仍然是我们所有基因组资源的中心。自十五年前首次设计以来，公开可用的基因组、转录和蛋白质组数据集的数量已经大幅增长，DNA测序技术的不断进步加速了这一增长。最初的目的是为参考人类基因组提供注释，我们已经扩展了我们的框架，以支持所有物种的基因组以及更丰富的组装模型。与其他信息学资源的交叉引用链接便于使用各种流行的标识符如UniProt和RefSeq搜索我们的数据库。我们全面而强大的框架在一个位置存储了大量不同的基因组注释，作为其他团队生成和维护自己定制注释的平台。我们欢迎重用和贡献：我们的数据库和API是公开可用的，我们的所有源代码都是在http://github.com/Ensembl上使用许可的Apachev2.0许可证发布的，并且我们有一个活跃的开发人员邮件列表(http://www.ensembl.org/info/about/contact/index.html).数据库地址：http://www.ensembl.org
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl ‘Core’ database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list (http://www.ensembl.org/info/about/contact/index.html). Database URL: http://www.ensembl.org