使用分布式注释系统和自动序列注释管道更新注释。
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.
机构信息
Medical Imaging Informatics Group, University of California, Los Angeles, CA, USA.
出版信息
Bioinformatics. 2012 Nov 1;28(21):2858-9. doi: 10.1093/bioinformatics/bts530. Epub 2012 Sep 3.
SUMMARY
The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing the output using the Distributed Annotation System (DAS) protocol. This interface allows pipeline plans in ASAP to be integrated into any system using HTTP and also allows the information returned by ASAP to be included in the DAS registry for use in any DAS-aware system. Three example implementations have been developed: the first accesses TRANSFAC information to automatically create gene sets for the Coordinated Gene Activity in Pattern Sets (CoGAPS) algorithm; the second integrates annotations from multiple array platforms and provides unified annotations in an R environment; and the third wraps the UniProt database for integration with the SPICE DAS client.
AVAILABILITY
Source code for ASAP 2.7 and the DAS 1.6 interface is available under the GNU public license. Proserver 2.20 is free software available from SourceForge. Scripts for installation and configuration on Linux are provided at our website: http://www.rits.onc.jhmi.edu/dbb/custom/A6/
摘要
BioDAS ProServer 与自动化序列注释管道 (ASAP) 的集成提供了一个接口，用于查询各种注释源，链接和链接结果，并使用分布式注释系统 (DAS) 协议标准化输出。该接口允许 ASAP 中的管道计划集成到任何使用 HTTP 的系统中，并且还允许 ASAP 返回的信息包含在 DAS 注册表中，以便在任何支持 DAS 的系统中使用。已经开发了三个示例实现：第一个访问 TRANSFAC 信息，以自动为协调基因活动模式集 (CoGAPS) 算法创建基因集；第二个集成来自多个数组平台的注释，并在 R 环境中提供统一的注释；第三个包装了 UniProt 数据库，以便与 SPICE DAS 客户端集成。
可用性
ASAP 2.7 和 DAS 1.6 接口的源代码可根据 GNU 公共许可证获得。Proserver 2.20 是可从 SourceForge 获得的免费软件。有关在 Linux 上进行安装和配置的脚本可在我们的网站上获得：http://www.rits.onc.jhmi.edu/dbb/custom/A6/
Zotero 插件