AustralieFrV1, Main, Exploration, bibRecord, 007F76

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

Identifieur interne : 007F76 ( Main/Exploration ); précédent : 007F75; suivant : 007F77

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

Auteurs : Jan Hannemann [Allemagne, Canada] ; Hendrik Poorter [Pays-Bas] ; Björn Usadel [Allemagne] ; Oliver E. Bl Sing [Allemagne] ; Alex Finck [Allemagne] ; Francois Tardieu [France] ; Owen K. Atkin [Australie] ; Thijs Pons [Canada] ; Mark Stitt [Allemagne] ; Yves Gibon [Allemagne, France]

Source :

Plant, cell and environment : (Print) [ 0140-7791 ] ; 2009.

RBID : Pascal:09-0362703

Descripteurs français

Pascal (Inist)
- Plan expérience, Interface, Génotype, Environnement, Perturbation, Plan échantillonnage, Bioinformatique, Traitement donnée, Fouille donnée, Ontologie, <<>>, Ecologie végétale.

English descriptors

KwdEn :
- Bioinformatics, Data mining, Data processing, Environment, Experimental design, Genotype, Interface, Ontology, Perturbation, Plant ecology, Sampling design.

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.

Affiliations:

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Le document en format XML

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<front><div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
<affiliations><list><country><li>Allemagne</li>
<li>Australie</li>
<li>Canada</li>
<li>France</li>
<li>Pays-Bas</li>
</country>
<region><li>Aquitaine</li>
<li>Berlin</li>
<li>Brandebourg</li>
<li>Languedoc-Roussillon</li>
<li>Nouvelle-Aquitaine</li>
<li>Occitanie (région administrative)</li>
<li>Utrecht (province)</li>
</region>
<settlement><li>Berlin</li>
<li>Bordeaux</li>
<li>Montpellier</li>
<li>Potsdam</li>
<li>Utrecht</li>
</settlement>
<orgName><li>Université d'Utrecht</li>
<li>Université de Bordeaux</li>
</orgName>
</list>
<tree><country name="Allemagne"><region name="Brandebourg"><name sortKey="Hannemann, Jan" sort="Hannemann, Jan" uniqKey="Hannemann J" first="Jan" last="Hannemann">Jan Hannemann</name>
</region>
<name sortKey="Bl Sing, Oliver E" sort="Bl Sing, Oliver E" uniqKey="Bl Sing O" first="Oliver E." last="Bl Sing">Oliver E. Bl Sing</name>
<name sortKey="Bl Sing, Oliver E" sort="Bl Sing, Oliver E" uniqKey="Bl Sing O" first="Oliver E." last="Bl Sing">Oliver E. Bl Sing</name>
<name sortKey="Finck, Alex" sort="Finck, Alex" uniqKey="Finck A" first="Alex" last="Finck">Alex Finck</name>
<name sortKey="Gibon, Yves" sort="Gibon, Yves" uniqKey="Gibon Y" first="Yves" last="Gibon">Yves Gibon</name>
<name sortKey="Stitt, Mark" sort="Stitt, Mark" uniqKey="Stitt M" first="Mark" last="Stitt">Mark Stitt</name>
<name sortKey="Usadel, Bjorn" sort="Usadel, Bjorn" uniqKey="Usadel B" first="Björn" last="Usadel">Björn Usadel</name>
</country>
<country name="Canada"><noRegion><name sortKey="Hannemann, Jan" sort="Hannemann, Jan" uniqKey="Hannemann J" first="Jan" last="Hannemann">Jan Hannemann</name>
</noRegion>
<name sortKey="Pons, Thijs" sort="Pons, Thijs" uniqKey="Pons T" first="Thijs" last="Pons">Thijs Pons</name>
</country>
<country name="Pays-Bas"><region name="Utrecht (province)"><name sortKey="Poorter, Hendrik" sort="Poorter, Hendrik" uniqKey="Poorter H" first="Hendrik" last="Poorter">Hendrik Poorter</name>
</region>
</country>
<country name="France"><region name="Occitanie (région administrative)"><name sortKey="Tardieu, Francois" sort="Tardieu, Francois" uniqKey="Tardieu F" first="Francois" last="Tardieu">Francois Tardieu</name>
</region>
<name sortKey="Gibon, Yves" sort="Gibon, Yves" uniqKey="Gibon Y" first="Yves" last="Gibon">Yves Gibon</name>
</country>
<country name="Australie"><noRegion><name sortKey="Atkin, Owen K" sort="Atkin, Owen K" uniqKey="Atkin O" first="Owen K." last="Atkin">Owen K. Atkin</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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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

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

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