Dataset Information

PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context.

ABSTRACT:

Background

Renewed interest in plant×environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community.

Description

PHENOPSIS DB is a publicly available (URL: http://bioweb.supagro.inra.fr/phenopsis/) information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i) the visualisation of environmental data of an experiment, (ii) the visualisation and statistical analysis of phenotypic data, and (iii) the analysis of Arabidopsis thaliana plant images.

Conclusions

Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype×environment interactions.

SUBMITTER: Fabre J

PROVIDER: S-EPMC3112076 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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Publications

PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context.

Fabre Juliette J Dauzat Myriam M Nègre Vincent V Wuyts Nathalie N Tireau Anne A Gennari Emilie E Neveu Pascal P Tisné Sébastien S Massonnet Catherine C Hummel Irène I Granier Christine C

BMC plant biology 20110509

<h4>Background</h4>Renewed interest in plant×environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis ...[more]

PMID: 21554668

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Dataset Information

PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context.

Background

Description

Conclusions

Publications

PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context.

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