Lyne Rachel, Sullivan Julie, Butano Daniela, Contrino Sergio, Heimbach Joshua, Hu Fengyuan, Kalderimis Alex, Lyne Mike, Smith Richard N, Štěpán Radek, Balakrishnan Rama, Binkley Gail, Harris Todd, Karra Kalpana, Moxon Sierra A T, Motenko Howie, Neuhauser Steven, Ruzicka Leyla, Cherry Mike, Richardson Joel, Stein Lincoln, Westerfield Monte, Worthey Elizabeth, Micklem Gos
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.
Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
Genesis. 2015 Aug;53(8):547-60. doi: 10.1002/dvg.22869. Epub 2015 Jul 8.
InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community.
InterMine是一个为大型复杂生物数据集开发的数据集成仓库和分析软件系统。它专为综合分析而设计，可通过用户友好的网络界面访问。对于生物信息学家而言，广泛的网络服务以及针对大多数常见脚本语言的编程接口支持对所有功能的访问。网络界面包括一个有用的标识符查找系统，以及简单和复杂的搜索选项。交互式结果表便于进行探索，数据可以进行过滤、汇总和浏览。一组图形分析工具为数据探索提供了丰富的环境，包括对基因集或其他实体的统计富集分析。InterMine数据库已针对主要模式生物（芽殖酵母、线虫、果蝇、斑马鱼、小鼠和大鼠）以及新开发的人类数据库进行了开发。在此，我们描述了这如何促进跨生物体分析工具和报告的互操作与开发。还介绍了InterMine作为数据探索和分析工具的情况。本文中描述的所有基于InterMine的系统都是科学界可免费使用的资源。
