Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB

通过 PlantGDB 进行（比较）植物基因组研究的网络基础设施

• 批准号: 0606909
• 负责人: Volker Brendel
• 金额: $ 346.96万
• 依托单位: Iowa State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-15 至 2011-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0606909&HistoricalAwards=false
• 关键词: Cyberinfrastructure; Comparative; Plant; Genome; Research

Proposal Title: Cyberinfrastructure for (Comparative) Plant Genome ResearchThrough PlantGDBInstitution: Iowa State UniversityAbstract Date: 05/31/2006PI Volker Brendel Iowa State UniversitySenior Personnel Qunfeng Dong Iowa Sate UniversityCo-PI Carolyn Lawrence Iowa State UniversityCo-PI Carol Lushbough University of South DakotaAccurate and comprehensive gene structure annotation in emerging and assembled genomes is fundamental to comparative, functional, and translational genomics. We propose to build the cyberinfrastructure necessary for defining and accessing the plant gene space. Our PlantGDB resource (www.plantgdb.org) will serve as a portal to plant genomic sequence data. Expressed sequence tags (ESTs) from all species will be presented in a uniform format and will undergo a standard procedure for clustering, assembly, and tentative annotation. The resulting putative unique transcripts (PUTs) will be mapped to their native and closely related genomes using specifically trained tools for spliced alignment. Predicted gene structures will be viewable on dedicated Web-based genome browsers, which also provide the opportunity for users to refine existing and contribute novel gene structure annotations. Confirmed gene structureannotations will be the data source for detailed studies of transcriptional regulation, including alternative splicing and the interplay of multiple types of mRNA processing. These data will also enable detection, display, and analysis of synteny among plant genomes. Through novel Web-interfaces, users will have a large range of query options to the underlying relational database. The PlantGDB-associated BioExtract Server (www.bioextract.org) tool provides simultaneous access to other remote data sets and capabilities to analyze selected data sets in user-defined workflows. Extensive development of Web services will integrate PlantGDB as a node in the emerging network of plant databases and resources.The PlantGDB resource is widely used and would continue to provide valuable data and analysis capabilities to the plant research community. A number of collaborative projects rely on PlantGDB for large-scale analyses and display of their data. PlantGDB hosts the Plant Genome Research Outreach Portal (PGROP, www.plantgdb.org/PGROP), a Web site providing access to a large number of resources and successful outreach programs. We plan to work with outreach coordinators from our campuses and nationwide to increase content and visibility of PGROP. We will also be working with colleagues in community and tribal colleges in South Dakota with the goal of increasing participation of their communities in plant genome research and building a bridge between plant genomics and ethobotany.Access to project outcomes: The primary web sites for this project are www.plantgdb.org and www.plantgdb.org/PGROP.

提案标题：(比较)植物基因组研究的网络基础设施通过PlantGDB机构：爱荷华州立大学摘要日期：05/31/2006 PI Volker Brendel Iowa State University高级人员东爱荷华州立大学Co-Pi Carolyn Lawrence Iowa State University南达科他州Co-PiCarol Lushbough大学在新兴基因组和组装基因组中准确和全面的基因结构注释是比较基因组学、功能基因组学和翻译基因组学的基础。我们建议建立定义和访问植物基因空间所需的网络基础设施。我们的PlantGDB资源(www.PLANGDB.org)将成为获取植物基因组序列数据的门户。来自所有物种的表达序列标签(EST)将以统一的格式呈现，并将经历标准的聚类、组装和试探性注释程序。由此产生的假定的独特转录本(Put)将使用专门训练的剪接比对工具被映射到它们的天然和密切相关的基因组。预测的基因结构将可以在专用的基于网络的基因组浏览器上看到，这也为用户提供了完善现有的和贡献新的基因结构注释的机会。确认的基因结构注释将成为详细研究转录调控的数据来源，包括选择性剪接和多种类型的信使核糖核酸加工的相互作用。这些数据还将使检测、显示和分析植物基因组之间的同步性成为可能。通过新颖的Web界面，用户将拥有对底层关系数据库的多种查询选择。PlantGDB相关的BioExtract服务器(www.BioExt.org)工具提供对其他远程数据集的同时访问，并提供在用户定义的工作流程中分析选定数据集的功能。Web服务的广泛开发将把PlantGDB整合为新兴的植物数据库和资源网络中的一个节点。PlantGDB资源得到了广泛的使用，并将继续为植物研究社区提供有价值的数据和分析能力。许多协作项目依赖PlantGDB进行大规模数据分析和显示。PlantGDB拥有植物基因组研究推广门户网站(PGROP，www.PLANGDB.org/PGROP)，该网站提供对大量资源和成功推广计划的访问。我们计划与我们校园和全国的外展协调员合作，提高PGROP的内容和知名度。我们还将与南达科他州社区和部落大学的同事合作，目标是让他们的社区更多地参与植物基因组研究，并在植物基因组学和民族植物学之间建立一座桥梁。获得项目成果：该项目的主要网站是www.ants gdb.org和www.ants gdb.org/pgrop。