ABI Development: The Arabidopsis Information Portal

小型植物拟南芥（Arabidopsis thaliana）是一种“模式生物”，作为其他植物的模式而被深入研究。该项目将开发拟南芥信息门户（AIP），这是一个新的资源，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单一的、用户友好的位置。它将采用一种模块化的联合模式，确保生成和维护有价值数据的责任仍然掌握在各个数据提供者手中，并将支持这些资源的负担分散到可能范围更广的资助机构和国家。AIP将由一个在科学基础设施、数据集成和社区参与方面具有丰富经验的团队开发，并将利用美国国家科学基金会在植物生物学研究界的重大投资。新AIP的关键要素包括开发模块化、社区可扩展的基于web的界面，该界面将包括可配置数据检索、分析和可视化应用程序的用户工作空间，实现InterMine的拟南芥特定实例，这是一个在动物模型生物数据库社区广泛接受的数据集成平台，以及设计和构建便于数据访问的web服务层。与iPlant协作资源的集成，与其他数据提供者的联合，以及分析工作流的开发。该项目将实施可持续发展战略，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。几十年来，拟南芥（Arabidopsis thaliana）一直被认为是植物研究的模式生物，是第一个完成基因组测序的植物物种。在过去的12年里，拟南芥信息资源（the Arabidopsis Information Resource， TAIR）作为收集、整理和传播有关该生物基因组、基因、突变体和其他信息的中心资源，服务于一个庞大的全球研究科学家、教育工作者和学生社区。TAIR数据库每月有超过3.6万的独立访客和180万的页面浏览量。随着TAIR的退休，AIP将承担类似的角色，但有新的职责范围。除了为社区提供更广泛、更丰富的数据集，包括基因组、表观基因组、转录组、蛋白质组、代谢组和表型数据外，AIP还将与iPlant项目合作，提供一套复杂的工具，可用于分析、可视化和解释数据。AIP将延续TAIR的模式，与植物科学界以及K-12、社区学院和4年制大学的学生和教育工作者进行教育合作。它将在适当的国家会议上审查和展示发展中的AIP功能，并为新工具和资源的潜在开发人员举办讲习班。AIP不仅将使拟南芥社区的生物信息学能力现代化，还将为建立和资助生物信息学能力的多机构、多国合作提供基础。

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.