Baxter Ivan, Ouzzani Mourad, Orcun Seza, Kennedy Brad, Jandhyala Shrinivas S, Salt David E
Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA.
Plant Physiol. 2007 Feb;143(2):600-11. doi: 10.1104/pp.106.092528. Epub 2006 Dec 22.
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.
高通量表型分析技术的出现产生了大量信息，如果没有适当的数据管理工具，这些信息将难以处理。这些数据管理工具应集成针对基因组规模数据采集与验证、数据存储与检索以及数据分析的既定工作流程控制，围绕感兴趣生物体的基因组信息建立索引。为了使这些大型数据集的影响力最大化，至关重要的是将它们迅速传播到更广泛的研究群体，允许开放获取以进行数据挖掘和发现。我们在此描述一个围绕普渡大学高通量离子组学表型分析平台开发的具备此类功能的系统。普渡大学离子组学信息管理系统（PiiMS）提供集成的工作流程控制、数据存储和分析，以促进高通量数据采集，同时还提供用于数据搜索、检索和可视化以进行假设开发的集成工具。PiiMS作为一个基于万维网的系统进行部署，允许集成分布式工作流程，并开放获取原始数据以供众多实验室进行分析。PiiMS目前包含来自拟南芥（Arabidopsis thaliana）超过60000个地上部组织样本中磷、钙、钾、镁、铜、铁、锌、锰、钴、镍、硼、硒、钼、钠、砷和镉的地上部浓度数据，包括甲磺酸乙酯、快中子和特定T-DNA突变体，以及来自800多个独立实验的自然种质和重组自交系群体，代表了超过100万个完全定量的元素浓度。可通过www.purdue.edu/dp/ionomics访问PiiMS。
