PHENOPSIS DB: an Information System for Arabidopsis thaliana 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 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

ALFIs: Alcoholic Fermentation Information System

il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : SOFTWAREIt is a scientific Information System dedicated to the study of alcoholic fermentation. It allows acquisition, annotation, consultation of the on-line or off-line measurements. Alfis also handles complex data and the description of winemaking operations. Thousands of fermentations done at the UMR SPO in Montpellier (volume 1L) and the experimental unit of Pech-Rouge Gruissan (volume 100L) are accessible via a dedicated website. Alfis also allows real-time monitoring of fermentation on the sites of Montpellier and Pech-Rouge.Alfis est un système d'information scientifique dédié à l'étude de la fermentation alcoolique. Il permet l'acquision, l'annotation, la consultation des mesures en ligne ou hors ligne. Alfis gère également les données complexes (par exemple des comptages) ainsi que la desciption fine des opérations oenologiques. Plusieurs milliers de fermentations réalisées à l'UMR SPO de Montpellier (volume 1 L ) ainsi qu'à l'unité expérimentale de Pech Rouge à Gruissan (volume 100l) sont accessibles via un site WEB dédié. Alfis permet également le suivi en temps réel des fermentations sur les sites de Montpellier et Pech Rouge

SILEX-VitiOeno

Le framework VitiOeno est le cœur de plusieurs Systèmes d'Information dédiés à la gestion de données viticole. Parmi les extensions réalisées et en production à ce jour, nous trouvons SystemVigne de l'UMR SYSTEM et les Systèmes d'Information des projets Vinnotec Pech-Rouge et Pilotype

Using annotations for R function management, MOQA : Méta-données et Ontologies pour la Qualité des Annotations

International audienc

Using ontologies of software : example of R functions management

International audienceIn a scientific context, making available scientific resources like computer programs is a real challenge for multidisciplinary research teams. In this paper, we propose an ontology-based approach to manage, share, reuse and promote software programs in a research community. Specifically, we were interested in the capitalization of R functions, R being a language for statistics and graphics. We designed an ontology to annotate R functions. We adopted the Semantic Web models: annotations are represented into the Resource Description Framework and the ontology in the Ontology Web Language. In the so-built semantic repository, R functions can be retrieved by expressing semantic queries in the SPARQL language. As a result, we have developed a new kind of software repository with semantic inferences. It is based upon the Corese semantic search engine and accessible through a Web Service. It has been adopted by a multidisciplinary team in life sciences

Using ontologies of software : example of R functions management

International audienceIn a scientific context, making available scientific resources like computer programs is a real challenge for multidisciplinary research teams. In this paper, we propose an ontology-based approach to manage, share, reuse and promote software programs in a research community. Specifically, we were interested in the capitalization of R functions, R being a language for statistics and graphics. We designed an ontology to annotate R functions. We adopted the Semantic Web models: annotations are represented into the Resource Description Framework and the ontology in the Ontology Web Language. In the so-built semantic repository, R functions can be retrieved by expressing semantic queries in the SPARQL language. As a result, we have developed a new kind of software repository with semantic inferences. It is based upon the Corese semantic search engine and accessible through a Web Service. It has been adopted by a multidisciplinary team in life sciences

Thanks to

e Stefania Palmieri, Studio legale Antartide, all migrants who let us try to understand what kind of places CIEs are. A project by eacea- eDucation, Audiovisual and Culture Executive Agency Seminars and round tables. Europeanisation of asylum and immigration law: detention and detention centres after the return directive. This project has been funded with support from the European Commission. This publication reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein. For further informatio