Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy

Authors

  • JAN HANNEMANN,

    Corresponding author
    1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany,
    2. University of Victoria, Centre for Forest Biology, PO Box 3020 STN CSC Victoria, Canada BC V8W 3N5,
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  • HENDRIK POORTER,

    1. Institute of Environmental Biology, Utrecht University, PO Box 800.84, 3508 TB Utrecht, The Netherlands,
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  • BJÖRN USADEL,

    1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany,
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  • OLIVER E. BLÄSING,

    1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany,
    2. Metanomics GmbH, Tegeler Weg 33, D-10589 Berlin, Germany,
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  • ALEX FINCK,

    1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany,
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  • FRANCOIS TARDIEU,

    1. INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 2 Place Viala, F-34820 Montpellier, France,
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  • OWEN K. ATKIN,

    1. Ecosystem Dynamics Group, Research School of Biological Sciences, Australian National University, Canberra, ACT 2602, Australia and
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  • THIJS PONS,

    1. University of Victoria, Centre for Forest Biology, PO Box 3020 STN CSC Victoria, Canada BC V8W 3N5,
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  • MARK STITT,

    1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany,
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  • YVES GIBON

    Corresponding author
    1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany,
    2. INRA-Bordeaux, Université de Bordeaux, UMR619 Biologie du Fruit, 71 Avenue Edouard Bourlaux, F-33883 Villenave d'Ornon, France
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J. Hannemann. e-mail: jaha@uvic.ca. Y. Gibon. e-mail: ygibon@bordeaux.inra.fr

ABSTRACT

Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive graphical interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.

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