IPGA: Gramene - Exploring Function through Comparative Genomics and Network Analysis

项目负责人：Doreen Ware（冷泉港实验室）合作负责人：Pankaj Jaiswal（俄勒冈州立大学）高级人员：Paul Kersey和Helen Parkinson（欧洲分子生物学实验室-欧洲生物信息学研究所），Lincoln Stein（安大略省癌症研究所）和Crispin Taylor（美国植物生物学家协会）Peter D’eustachio（纽约大学医学院），Joshua Stein（冷泉港实验室）和Palitha Dharmawardhana（俄勒冈州立大学）植物生物学的研究正在达到一个临界点，在这个临界点上，检查整个系统的设施，增加信息的整合，以及对实验数据的更复杂的分析，都准备好了在知识和洞察力方面取得全面的进步。与此同时，对植物基因组的理解和新信息技术的进步正在改变进行植物科学研究的速度、规模和策略，例如，允许对基因、环境和植物形态和功能之间的联系有更丰富的认识。植物科学的这些进步有望彻底改变作物育种，并有助于跟上未来人口增长、环境压力和能源需求的步伐。在过去的十年中，Gramene （www.gramene.org）数据库已经成为研究界了解多种植物物种基因结构和功能信息的门户。Gramene门户网站提供的工具允许研究人员使用标准化框架，在最新信息和分析的基础上提出新的假设。然而，还有许多机会可以更充分地利用来自不同植物物种的功能信息。在这个项目中，Gramene将大幅增加整合到门户网站的植物基因组数量，增加研究基因表达、途径和网络的新功能，并从根本上改进数据库架构和用户界面，以促进复杂的系统级分析。至少有20个参考基因组，由研究它们的科学家注释，包括农作物、模式生物和其他物种，将被纳入扩展的Gramene门户网站。水稻、玉米和拟南芥将通过增加来自表达、表观基因组和全基因组关联研究（GWAS）的公开数据来强调。通过与Ensembl Plants项目（plants.ensembl.org）的合作，将维护这些数据类型的单一国际协调资源。为了更好地获取有关植物基因功能的信息，Gramene将采用两种强大的工具：Reactome （www.reactome.org）平台，可用于表示经过整理的途径并执行基于途径的分析；ATLAS （www.ebi.ac.uk/gxa/）平台，可用于显示和分析表达谱。这些接口，连同Ensembl、BioMart和GWAS查看器，将形成一个集成的分析系统，该系统建立在结构化元数据之上，并通过大容量数据仓库和高级搜索引擎实现。为了吸引和培养早期职业科学家，该项目将为博士后助理和各级学生提供研究培训机会。将通过在国际出席的会议上举行的介绍和讲习班来完成关于使用格拉梅工具的培训；将通过一系列网络研讨会接触到更广泛的受众。另一个主要目标是在社区资源之间实现广泛的互操作性。标准的制定将通过与几个nsf支持的研究协调网络（rcn）确定的协作数据伙伴和科学家的联系来完成。建立共同的协议、词汇和语义将对国内外科研和教育领域的科学家聚集在一起产生强大的影响。进一步的目标是吸引在各自领域最具资格的生物学家在实验证据的基础上为基因组注释做出贡献。Gramene将每年举办一次研讨会，培训科学家使用标准的管理工具，这些工具可以产生数据类型和元数据的一致定义。最后，无处不在的同行评议期刊的在线出版为更好地将基因组数据库与科学文献联系起来提供了新的机会。Gramene将与两家高影响力期刊的出版商美国植物生物学家协会（ASPB）合作，开发将结构化实验数据收集与手稿接受和出版过程结合起来的方法原型。总体而言，该项目将有助于将信息科学与自然科学相结合的长期进展，最终将对技术和社会产生积极影响。

PI: Doreen Ware (Cold Spring Harbor Laboratory)Co-PI: Pankaj Jaiswal (Oregon State University) Senior Personnel: Paul Kersey and Helen Parkinson (European Molecular Biology Laboratory-European Bioinformatics Institute), Lincoln Stein (Ontario Institute for Cancer Research) and Crispin Taylor (American Society of Plant Biologists)Key Collaborators: Peter D'Eustachio (New York University School of Medicine), Joshua Stein (Cold Spring Harbor Laboratory) and Palitha Dharmawardhana (Oregon State University)Research in plant biology is reaching a tipping point at which the facility to examine entire systems, increasing integration of information, and ever more sophisticated analyses of experimental data are poised to enable sweeping advances in knowledge and insight. Meanwhile, progress in understanding plant genomes and novel information technologies are transforming the pace, scale, and strategies used to conduct plant science research, allowing, for example, much richer appreciation for the connections among genes, environments, and plant form and function. These advances in plant science promise to revolutionize crop breeding and help to keep pace with future population growth, environmental pressures, and energy needs. In the past decade, the Gramene (www.gramene.org) database has served the research community as a portal to information about gene structure and function for multiple plant species. Tools offered through the Gramene portal allow researchers to develop novel hypotheses on the bases of the most recent information and analyses, using a standardized framework. Yet, there are many remaining opportunities to more fully leverage functional information available from diverse plant species. In this project, Gramene will substantially expand the number of plant genomes incorporated into the portal, add new capabilities for studying gene expression, pathways, and networks, and fundamentally improve the database architecture and user interfaces to facilitate sophisticated systems-level analyses. At least twenty reference genomes, annotated by the scientists who are studying them and including crop plant, model organism, and other species, will be incorporated into the expanded Gramene portal. Rice, maize, and Arabidopsis will be emphasized through the addition of publicly available data from expression, epigenomic, and genome-wide association studies (GWAS). A single internationally-coordinated resource for these data types will be maintained through collaboration with the Ensembl Plants project (plants.ensembl.org). To better capture information about the function of plant genes, Gramene will adopt two powerful tools: the Reactome (www.reactome.org) platform, which can be used to represent curated pathways and for performing pathways-based analyses; and the ATLAS (www.ebi.ac.uk/gxa/) platform, which can be used to display and analyze expression profiles. These interfaces, along with Ensembl, BioMart, and a GWAS viewer, will form an integrated analysis system that is built on structured metadata and implemented through a high-capacity data warehouse and an advanced search engine.To engage and nurture early career scientists, the project will provide research training opportunities for postdoctoral associates and students at all levels. Training on the use of Gramene tools will be accomplished through presentations and workshops held at internationally attended conferences; broader audiences will be reached through a series of webinars. Another major objective is to achieve broad interoperability among community resources. Standards development will be accomplished via outreach to collaborative data partners and scientists identified through several NSF-supported Research Coordination Networks (RCNs). Establishing common protocols, vocabularies, and semantics will have the powerful effect of bringing scientists together in research and educational fields, both domestically and abroad. A further objective is to engage biologists who are best qualified in their field to contribute to genome annotations on the basis of experimental evidence. Gramene will hold annual jamborees to train scientists in the use of standard curation tools that produce consistent definitions of data types and metadata. Finally, the ubiquitous publication of peer-reviewed journals online enables new opportunities to better link genome databases with the scientific literature. Gramene will collaborate with the American Society of Plant Biologists (ASPB), publisher of two high-impact journals, to prototype ways to couple collection of structured experimental data to the manuscript acceptance and publication process. As a whole, this project will contribute to long-term progress in merging information sciences with natural sciences that will ultimately lead to positive impacts on technology and society.