ABI Development: The Arabidopsis Information Portal

ABI 开发：拟南芥信息门户

• 批准号: 1262414
• 负责人: Christopher Town
• 金额: $ 449.29万
• 依托单位: J. Craig Venter Institute, Inc.
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-15 至 2018-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1262414&HistoricalAwards=false
• 关键词: ABI; Development; Arabidopsis; Information; Portal

The small plant Arabidopsis thaliana is a "model organism" that is studied in great depth as a model for other plants. This project will develop the Arabidopsis Information Portal (AIP), a new resource to bring together the ever-increasing amounts of Arabidopsis data into a single, user-friendly location using the latest web technologies and web services. It will adopt a modular, federated model which ensures that responsibility for generation and maintenance of valuable data remains in the hands of the individual data providers and spreads the burden of supporting such resources across a potentially wider range of funding agencies and countries. The AIP will be developed by a team with deep experience in scientific infrastructure, data integration, and community engagement, and will take advantage of significant NSF investments in the plant biology research community. Key elements of the new AIP include the development of modular, community-extensible web-based interface that will include user work spaces that can be configured with data retrieval, analysis, and visualization applications, implementation of an Arabidopsis-specific instance of InterMine, a data integration platform that is widely accepted in the animal model organism database community, and the design and construction of a web services layer that facilitates data access, integration with iPlant Collaborative resources, federation with other data providers, and development of analytical workflows. The project will implement a sustainability strategy that embraces adoption of existing scientific infrastructure, use of virtualization, federated provision of data, collaborative development of new resources, and pursuit of alternative funding sources. Arabidopsis thaliana has been recognized as a model organism for plant research for many decades and was the first plant species to have a fully sequenced genome. For the past twelve years, The Arabidopsis Information Resource (TAIR) has served a large, worldwide community of research scientists, educators and students as a central resource collecting, curating and disseminating information about the organism's genome, genes, mutants and other information. The TAIR database receives over 36,000 unique visitors and 1.8 million page views per month. With the retirement of TAIR, the AIP will take on a similar role but with a new spectrum of responsibilities. In addition to providing the community with facile access to broader and richer data sets, including genomic, epigenomic, transcriptomic, proteomic, metabolomic and phenomic data, the AIP will cooperate with the iPlant project to provide access to a sophisticated suite of tools that can be used to analyze, visualize, and interpret the data. The AIP will continue the TAIR model of educational engagement with the plant science community and with students and educators at the K-12, Community College and 4 year college level. It will provide reviews and demonstrations of the developing AIP functionalities at appropriate national meetings and host workshops for potential developers of new tools and resources. Not only will AIP modernize the bioinformatics capacity of the Arabidopsis community, it will provide a foundation for multi-agency, multi-national collaboration in building and funding biological informatics capabilities.

小植物拟南芥是一种被作为其他植物的模式进行深入研究的“模式生物”。该项目将开发拟南芥信息门户(AIP)，这是一种新的资源，利用最新的网络技术和网络服务，将不断增加的拟南芥数据汇集到一个用户友好的单一位置。它将采用模块化的联合模式，确保有价值数据的生成和维护责任仍然掌握在各个数据提供者手中，并将支助这类资源的负担分摊给可能范围更广的供资机构和国家。AIP将由一个在科学基础设施、数据集成和社区参与方面拥有丰富经验的团队开发，并将利用NSF在植物生物学研究社区的重大投资。新的AIP的关键要素包括开发模块化的、社区可扩展的基于网络的界面，其中将包括可配置数据检索、分析和可视化应用的用户工作空间，实施Intermine的拟南芥实例，一个被动物模型生物体数据库社区广泛接受的数据集成平台，以及设计和构建促进数据访问的网络服务层，与iPLANT协作资源的整合，与其他数据提供商的联合，以及分析工作流程的开发。该项目将实施一项可持续发展战略，包括采用现有的科学基础设施、使用虚拟化、联合提供数据、合作开发新资源以及寻求替代资金来源。拟南芥几十年来一直被认为是植物研究的模式生物，是第一个拥有全基因组测序的植物物种。在过去的12年里，拟南芥信息资源(TAIR)作为收集、管理和传播有关生物体基因组、基因、突变和其他信息的中心资源，为世界各地的研究科学家、教育工作者和学生社区提供了服务。TIIR数据库每月接待超过3.6万名独立访问者和180万页面浏览量。随着Tair的退休，AIP将承担类似的角色，但承担着新的职责范围。除了为社区提供更广泛和更丰富的数据集，包括基因组、表观基因组、转录组、蛋白质组、代谢组和表观组数据，AIP还将与iPLANT项目合作，提供对可用于分析、可视化和解释数据的一套复杂工具的访问。AIP将继续与植物科学界以及K-12、社区大学和四年制大学水平的学生和教育工作者进行教育接触的TIIR模式。它将在适当的国家会议上审查和演示正在开发的AIP功能，并为新工具和资源的潜在开发者举办讲习班。AIP不仅将使拟南芥社区的生物信息学能力现代化，还将为多机构、多国家在建设和资助生物信息学能力方面的合作提供基础。

项目成果

Araport: an application platform for data discovery: Araport: an application platform for data discovery

Araport：数据发现应用平台： Araport：数据发现应用平台

• DOI: 10.1002/cpe.3542
• 发表时间: 2015
• 期刊: Concurrency and Computation: Practice and Experience
• 作者: Hanlon, Matthew R.;Vaughn, Matthew;Mock, Stephen;Dooley, Rion;Moreira, Walter;Stubbs, Joe;Town, Chris;Miller, Jason;Krishnakumar, Vivek;Ferlanti, Erik
• 通讯作者: Ferlanti, Erik