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BIOINFORMATICS

Purdue Ionomics Information Management System. An Integrated Functional Genomics Platform^{1,[C],[W],[OA]}

Bindley Bioscience Center (I.B., D.E.S.), Cyber Center (M.O., B.K., S.S.J.), e-Enterprise Center (S.O.), and Horticulture and Landscape Architecture (I.B., D.E.S.), Purdue University, West Lafayette, Indiana 47907

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: David E. Salt (dsalt{at}purdue.edu).

^[C] Some figures in this article are displayed in color online but in black and white in the print edition.

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.092528

^* Corresponding author; e-mail dsalt{at}purdue.edu; fax 765–494–0391.

Received November 2, 2006; accepted December 12, 2006; published December 22, 2006.

This article has been cited by other articles:

				I. R. Baxter, O. Vitek, B. Lahner, B. Muthukumar, M. Borghi, J. Morrissey, M. L. Guerinot, and D. E. Salt The leaf ionome as a multivariable system to detect a plant's physiological status PNAS, August 19, 2008; 105(33): 12081 - 12086. [Abstract] [Full Text] [PDF]

				M. R. Broadley, J. P. Hammond, G. J. King, D. Astley, H. C. Bowen, M. C. Meacham, A. Mead, D. A.C. Pink, G. R. Teakle, R. M. Hayden, et al. Shoot Calcium and Magnesium Concentrations Differ between Subtaxa, Are Highly Heritable, and Associate with Potentially Pleiotropic Loci in Brassica oleracea Plant Physiology, April 1, 2008; 146(4): 1707 - 1720. [Abstract] [Full Text] [PDF]