Award details

13-NSFABI: Arabidopsis Information Portal

Reference	BB/L027151/1
Principal Investigator / Supervisor	Professor Gos Micklem
Co-Investigators / Co-Supervisors
Institution	University of Cambridge
Department	Genetics
Funding type	Research
Value (£)	382,301
Status	Completed
Type	Research Grant
Start date	01/01/2014
End date	31/08/2016
Duration	32 months

Abstract

The goal of the AIP team is to develop a next-generation Arabidopsis cyberinfrastructure that facilitates data aggregation and integration, presents a flexible and task- oriented user interface, and is modular and extensible. Wherever possible the AIP team will aim for integration of separate data sets over simple aggregation, thus enabling more sophisticated queries and analyses to be performed. Apart from data directly curated by the AIP core, a guiding principle of the project is that provision of data collections, such as transcriptomics and proteomics, should be the responsibility of domain experts who will make their data available to AIP in metadata-rich, standardized formats. AIP will collaborate with community data providers to facilitate integration of their data and analytical code into its framework. AIP will develop a user-customizable web portal that will enable queries across integrated data sets, bioinformatic analyses, and visualization of results. The default interface will replicate much of the functionality of TAIR, but will be configurable and extensible. Though the AIP is designated a 'portal' it is in aggregate a complete Arabidopsis-oriented cyberinfrastructure comprised of three major components: a Portal Layer to provide graphical access; a Data Layer, which will federate or integrate data repositories differing in type, content, and physical location; and a mediating Web Services Layer, based on InterMine and the iPlant Agave Web Services technologies, that will provide access to data sources and the national science infrastructure. This modular development strategy enables components to be easily replaced as new technologies emerge. Each component will communicate using standard protocols and will be developed using strategically aligned software practices.

Summary

For over a decade, The Arabidopsis Information Resource (TAIR) has served as a data and analysis resource for a community of thousands of Arabidopsis and other plant species' researchers. Supported by a Research Coordination Network grant, IAIC-sponsored meetings and workshops produced a concept for a new Arabidopsis Information Portal (AIP). This new resource portal is envisaged as a mechanism 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 development model which ensures that responsibility for generation and maintenance of valuable data to remains in the hands of the individual data providers and spreads the burden of supporting such resources across a potentially wider range of countries and funding agencies. 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. In addition to providing the community with 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. AIP will continue the TAIR model of educational engagement with the plant science community. 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.

Impact Summary

The proposed Arabidopsis-oriented cyberinfrastructure will serve the plant worldwide community, taking on and expanding the role of TAIR. This active community comprises research scientists, educators and students, with the TAIR web site currently receiving over 36,000 unique visitors and 1.8 million page views per month. Arabidopsis research is important both to basic plant science and to the breeding of commercial crops. The direct beneficiaries of this project will be found therefore both in the academic and the commercial sector, and the research facilitated by the project could have an impact on policy making and on the public in general.

Committee	Research Committee C (Genes, development and STEM approaches to biology)
Research Topics	Plant Science, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	NSF Arabidopsis Information (NSFABI) [2013]
Funding Scheme	X – not Funded via a specific Funding Scheme

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