NSF Award
1262414
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. <br/><br/>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.
