title: 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.
  
  
  METHODS
  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.
authors.affiliation: Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA-AGRO-M, UMR 759, 2 Place Viala, 34060 Montpellier Cedex 1 France.
authors.forename: Juliette
authors.initials: J
authors.lastname: Fabre
authors.forename: Myriam
authors.initials: M
authors.lastname: Dauzat
authors.forename: Vincent
authors.initials: V
authors.lastname: Nègre
authors.forename: Nathalie
authors.initials: N
authors.lastname: Wuyts
authors.forename: Anne
authors.initials: A
authors.lastname: Tireau
authors.forename: Emilie
authors.initials: E
authors.lastname: Gennari
authors.forename: Pascal
authors.initials: P
authors.lastname: Neveu
authors.forename: Sébastien
authors.initials: S
authors.lastname: Tisné
authors.forename: Catherine
authors.initials: C
authors.lastname: Massonnet
authors.forename: Irène
authors.initials: I
authors.lastname: Hummel
authors.forename: Christine
authors.initials: C
authors.lastname: Granier
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D016208:Databases, Factual; D004777:Environment; D005838:Genotype; D007091:Image Processing, Computer-Assisted; D020407:Internet; D010641:Phenotype; D018515:Plant Leaves / Q000033:anatomy & histology / Q000254:growth & development; D014584:User-Computer Interface