Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB

提案题目：通过植物进行（比较）植物基因组研究的网络基础设施机构：爱荷华州立大学摘要日期：2005年5月31日沃尔克·布伦德尔爱荷华州立大学高级人员董群峰爱荷华州立大学联合研究员卡罗琳·劳伦斯爱荷华州立大学联合研究员卡罗尔·卢斯堡南达科他州大学准确和全面的基因结构注释是比较、功能和翻译基因组学的基础。我们建议建立必要的网络基础设施来定义和访问植物基因空间。我们的PlantGDB资源（www.plantgdb.org）将作为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，并将经历聚类、组装和初步注释的标准程序。由此产生的假定的唯一转录本（put）将使用经过专门训练的剪接比对工具映射到它们的原生和密切相关的基因组。预测的基因结构将在专门的基于web的基因组浏览器上可见，这也为用户提供了改进现有基因结构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转录调控详细研究的数据来源，包括选择性剪接和多种mRNA加工类型的相互作用。这些数据也将使检测、显示和分析植物基因组之间的协同性成为可能。通过新颖的web界面，用户将拥有对底层关系数据库的大量查询选项。plantgdb相关的BioExtract Server （www.bioextract.org）工具提供对其他远程数据集的同时访问，并能够在用户定义的工作流中分析选定的数据集。Web服务的广泛发展将使PlantGDB成为新兴的植物数据库和资源网络中的一个节点。PlantGDB资源被广泛使用，并将继续为植物研究界提供有价值的数据和分析能力。许多合作项目依靠PlantGDB进行大规模分析和数据显示。PlantGDB拥有植物基因组研究推广门户网站（PGROP, www.plantgdb.org/PGROP），这是一个提供大量资源和成功推广计划的网站。我们计划与我们校园和全国的外展协调员合作，增加pgroup的内容和知名度。我们还将与南达科他州社区和部落学院的同事合作，目标是增加他们社区对植物基因组研究的参与，并在植物基因组学和植物植物学之间建立一座桥梁。获取项目成果：该项目的主要网站是www.plantgdb.org和www.plantgdb.org/PGROP。

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.