PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-05-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/11/77 |
| _version_ | 1818807765581168640 |
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| author | Massonnet Catherine Tisné Sébastien Neveu Pascal Gennari Emilie Tireau Anne Wuyts Nathalie Nègre Vincent Dauzat Myriam Fabre Juliette Hummel Irène Granier Christine |
| author_facet | Massonnet Catherine Tisné Sébastien Neveu Pascal Gennari Emilie Tireau Anne Wuyts Nathalie Nègre Vincent Dauzat Myriam Fabre Juliette Hummel Irène Granier Christine |
| author_sort | Massonnet Catherine |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>Arabidopsis thaliana</it>, 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 <it>Arabidopsis thaliana </it>phenotyping, with the scientific community.</p> <p>Description</p> <p>PHENOPSIS DB is a publicly available (URL: <url>http://bioweb.supagro.inra.fr/phenopsis/</url>) 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 <it>Arabidopsis thaliana </it>plant images.</p> <p>Conclusions</p> <p>Firstly, data stored in the PHENOPSIS DB are of interest to the <it>Arabidopsis thaliana </it>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.</p> |
| first_indexed | 2024-12-18T19:30:52Z |
| format | Article |
| id | doaj.art-29da0af561f74663a01a52f1da5398be |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-18T19:30:52Z |
| publishDate | 2011-05-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj.art-29da0af561f74663a01a52f1da5398be2022-12-21T20:55:44ZengBMCBMC Plant Biology1471-22292011-05-011117710.1186/1471-2229-11-77PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental contextMassonnet CatherineTisné SébastienNeveu PascalGennari EmilieTireau AnneWuyts NathalieNègre VincentDauzat MyriamFabre JulietteHummel IrèneGranier Christine<p>Abstract</p> <p>Background</p> <p>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 <it>Arabidopsis thaliana</it>, 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 <it>Arabidopsis thaliana </it>phenotyping, with the scientific community.</p> <p>Description</p> <p>PHENOPSIS DB is a publicly available (URL: <url>http://bioweb.supagro.inra.fr/phenopsis/</url>) 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 <it>Arabidopsis thaliana </it>plant images.</p> <p>Conclusions</p> <p>Firstly, data stored in the PHENOPSIS DB are of interest to the <it>Arabidopsis thaliana </it>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.</p>http://www.biomedcentral.com/1471-2229/11/77 |
| spellingShingle | Massonnet Catherine Tisné Sébastien Neveu Pascal Gennari Emilie Tireau Anne Wuyts Nathalie Nègre Vincent Dauzat Myriam Fabre Juliette Hummel Irène Granier Christine PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context BMC Plant Biology |
| title | PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context |
| title_full | PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context |
| title_fullStr | PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context |
| title_full_unstemmed | PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context |
| title_short | PHENOPSIS DB: an Information System for <it>Arabidopsis thaliana </it>phenotypic data in an environmental context |
| title_sort | phenopsis db an information system for it arabidopsis thaliana it phenotypic data in an environmental context |
| url | http://www.biomedcentral.com/1471-2229/11/77 |
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