Information Commons for Rice (IC4R).
Information Commons for Rice (IC4R).
复制标题
大米信息共享 (IC4R)
DOI：
10.1093/nar/gkv1141
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Xue Y
中科院分区：
文献类型：
--
作者：
IC4R Project Consortium;Hao L;Zhang H;Zhang Z;Hu S;Xue Y
水稻是世界上很大一部分人口最重要的主食，也是植物研究的关键模式生物。在此，我们介绍水稻信息共享平台（IC4R；http://ic4r.org），这是一个水稻知识库，其特点是采用了可扩展且可持续的架构，通过社区贡献的模块整合多种组学数据。每个模块由不同的专业团队开发和维护，负责数据收集、处理与可视化，并通过网络服务按需提供数据。在当前版本中，IC4R通过多个专业模块整合了各类水稻数据，包括完全源自RNA测序数据的全基因组表达谱、从数千个水稻品种重测序数据中获得的基于重测序的基因组变异、涵盖多种不同植物物种的植物同源基因、翻译后修饰、水稻相关文献以及水稻研究界贡献的基因注释。与现有相关数据库不同，IC4R在设计上注重可扩展性和可持续性，因此还具备水稻数据的协作整合以及数据库更新与维护成本低的特点。IC4R未来的发展方向包括纳入其他组学数据，以及将多种组学数据与重要农艺性状相关联，致力于将IC4R打造成一个对水稻基础研究和转化研究都有重要价值的知识库。
Rice is the most important staple food for a large part of the world's human population and also a key model organism for plant research. Here, we present Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and maintained by different committed groups, deals with data collection, processing and visualization, and delivers data on-demand via web services. In the current version, IC4R incorporates a variety of rice data through multiple committed modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community. Unlike extant related databases, IC4R is designed for scalability and sustainability and thus also features collaborative integration of rice data and low costs for database update and maintenance. Future directions of IC4R include incorporation of other omics data and association of multiple omics data with agronomically important traits, dedicating to build IC4R into a valuable knowledgebase for both basic and translational researches in rice.