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VarioML framework for comprehensive variation data representation and exchange.
Byrne M., Fokkema I., Lancaster O., Adamusiak T., Ahonen-Bishopp A., Atlan D., Béroud C., Cornell M., Dalgleish R., Devereau A. et al
BMC Bioinformatics 13, 1 (2012) 254 - http://www.hal.inserm.fr/inserm-00758018
 (23031277) 
VarioML framework for comprehensive variation data representation and exchange.
Myles Byrne1, Ivo Fokkema2, Owen Lancaster3, Tomasz Adamusiak4, Anni Ahonen-Bishopp5, David Atlan6, Christophe Béroud7, Michael Cornell8, Raymond Dalgleish3, Andrew Devereau8, George Patrinos9, Morris Swertz10, Peter Taschner2, Gudmundur Thorisson3, Mauno Vihinen11, 12, 13, Anthony Brookes3, Juha Muilu () 1
1 :  Institute for Molecular Medicine Finland (FIMM)
University of Helsinki
Helsinki
Finlande
2 :  Department of Human Genetics
Leiden University Medical Center
Leiden
Pays-Bas
3 :  Genetics Department
University of Leicester
University Road, Leicester LE1 7RH
Royaume-Uni
4 :  Medical College of Wisconsin
Medical College Of Wisconsin
Milwaukee, WI
États-Unis
5 :  Biocomputing Platforms, Ltd
Biocomputing Platforms, Ltd
Espoo
Finlande
6 :  Phenosystems Inc
Phenosystems Inc
Brussels
Belgique
7 :  Génétique Médicale et Génomique Fonctionnelle
INSERM : U910 – Université de la Méditerranée - Aix-Marseille II – Hôpital La Timone – Assistance publique - Hôpitaux de Marseille (AP-HM)
Faculté de Médecine - 27 boulevard Jean Moulin 13385 Marseille Cedex 05
France
8 :  National Genetics Reference Laboratory
National Genetics Reference Laboratory
Manchester
Royaume-Uni
9 :  Department of Pharmacy
University of Patras
School of Health Sciences,Patras
Grèce
10 :  Department of Genetics
University of Groningen
Genomics Coordination Center University Medical Center Groningen and Groningen Bioinformatics Center, Groningen
Pays-Bas
11 :  Department of Experimental Medical Science
Lund University
Lund
Suède
12 :  Institute of Biomedical Technology
University of Tampere
Tampere
Finlande
13 :  Tampere University Hospital
Tampere University Hospital
Finlande
ABSTRACT: BACKGROUND: Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. RESULTS: The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDB's) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. CONCLUSIONS: VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.
Sciences du Vivant/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique
Sciences du Vivant/Bio-Informatique, Biostatistique
Informatique/Bio-informatique
Anglais
1471-2105

Articles dans des revues avec comité de lecture
10.1186/1471-2105-13-254
BMC Bioinformatics (BMC Bioinformatics)
Publisher BioMed Central
ISSN 1471-2105 
internationale
03/10/2012
03/10/2012
13
1
254

LSDB – Variation database curation – Data collection – Distribution
Numéro Cordis 200754
Acronyme GEN2PHEN
Titre Genotype-To-Phenotype Databases: A Holistic Solution
Financé par HEALTH
Début 2008-01-01
Date de fin 2012-12-31
Identifiant de l'appel FP7-HEALTH-2007-A
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PDF
1471-2105-13-254.pdf(493.1 KB)
ANNEX
1471-2105-13-254.xml(80.5 KB)