Purdue ionomics information management system. An integrated functional genomics platform

Ivan Baxter, Mourad Ouzzani, Seza Orcun, Brad Kennedy, Shrinivas S. Jandhyala, David E. Salt

Research output: Contribution to journalArticle

91 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)600-611
Number of pages12
JournalPlant Physiology
Volume143
Issue number2
DOIs
Publication statusPublished - 1 Feb 2007
Externally publishedYes

Fingerprint

Management Information Systems
management information systems
Workflow
Information Storage and Retrieval
Genomics
genomics
Arabidopsis
Ethyl Methanesulfonate
Systems Integration
Fast Neutrons
data analysis
Data Mining
phenotype
world wide web
ethyl methanesulfonate
Internet
shoots
inbred lines
Technology
Arabidopsis thaliana

ASJC Scopus subject areas

  • Plant Science

Cite this

Purdue ionomics information management system. An integrated functional genomics platform. / Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S.; Salt, David E.

In: Plant Physiology, Vol. 143, No. 2, 01.02.2007, p. 600-611.

Research output: Contribution to journalArticle

Baxter, Ivan ; Ouzzani, Mourad ; Orcun, Seza ; Kennedy, Brad ; Jandhyala, Shrinivas S. ; Salt, David E. / Purdue ionomics information management system. An integrated functional genomics platform. In: Plant Physiology. 2007 ; Vol. 143, No. 2. pp. 600-611.
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