BibSonomy :: publication :: PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

Juliette Fabre, Myriam Dauzat, Vincent Negre, Nathalie Wuyts, Anne Tireau, Emilie Gennari, Pascal Neveu, Sebastien Tisne, Catherine Massonnet, Irene Hummel, and Christine Granier. BMC Plant Biology 11(1):77 (2011)

@article{21554668,
  abstract = {BACKGROUND:Renewed interest in plant x 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/ webcite) 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 x environment interactions.},
  added-at = {2012-09-17T19:15:33.000+0200},
  author = {Fabre, Juliette and Dauzat, Myriam and Negre, Vincent and Wuyts, Nathalie and Tireau, Anne and Gennari, Emilie and Neveu, Pascal and Tisne, Sebastien and Massonnet, Catherine and Hummel, Irene and Granier, Christine},
  biburl = {http://www.bibsonomy.org/bibtex/2cc39037f363b065f25378d63a25dd44c/b.bruns},
  description = {BMC Plant Biology | Full text | PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context},
  doi = {10.1186/1471-2229-11-77},
  interhash = {c89a82a5520bafea726c172644bdb6ac},
  intrahash = {cc39037f363b065f25378d63a25dd44c},
  issn = {1471-2229},
  journal = {BMC Plant Biology},
  keywords = {data_repository dbms phenopsis phenotyping},
  number = 1,
  pages = 77,
  pubmedid = {21554668},
  timestamp = {2012-09-17T19:15:33.000+0200},
  title = {PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context},
  url = {http://www.biomedcentral.com/1471-2229/11/77},
  volume = 11,
  year = 2011
}

%0 Journal Article
%1 21554668
%A Fabre, Juliette
%A Dauzat, Myriam
%A Negre, Vincent
%A Wuyts, Nathalie
%A Tireau, Anne
%A Gennari, Emilie
%A Neveu, Pascal
%A Tisne, Sebastien
%A Massonnet, Catherine
%A Hummel, Irene
%A Granier, Christine
%D 2011
%J BMC Plant Biology
%K 
%N 1
%P 77
%T PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context
%R 10.1186/1471-2229-11-77
%U http://www.biomedcentral.com/1471-2229/11/77
%V 11
%X BACKGROUND:Renewed interest in plant x 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/ webcite) 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 x environment interactions.

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DOI:	10.1186/1471-2229-11-77
URL:	http://www.biomedcentral.com/1471-2229/11/77
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BibTeX key:	21554668

abstract

BACKGROUND:Renewed interest in plant x 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/ webcite 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 x environment interactions.

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BMC Plant Biology | Full text | PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

publication post of b.bruns

PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

discussion

resources (URL, PDF, ...)

abstract

Description