Abstract
BackgroundRenewed 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.DescriptionPHENOPSIS 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.ConclusionsFirstly, 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.
Highlights
Renewed interest in plant × environment interactions has risen in the post-genomic era
Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce
The structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype × environment interactions
Summary
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. 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. In three highly controlled growth chambers, plants are subjected to different temperatures, day-lengths and drought treatments with an automatic recording of all environmental data In platforms such as this, large quantities of environmental data, plant images and phenotypic data are produced for the study of genotype × environment effects on different plant processes. We describe the content and utility of PHENOPSIS DB, an information system for the storage (database), analysis and sharing (Web interface, Web Services) of images and data collected in the PHENOPSIS platform
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