PMID: identifiant
de la référence Pubmed : |
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 (23031277)  |
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| titre : |
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VarioML framework for comprehensive variation data representation and exchange. |
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| auteur(s) : |
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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 |
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| laboratoire : |
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| résumé : |
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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. |
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| domaine : |
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langue du texte
intégral : |
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Anglais |
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| ISSN : |
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1471-2105 |
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| type de publication : |
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Articles dans des revues avec comité de lecture |
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| DOI : |
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10.1186/1471-2105-13-254 |
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| journal : |
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| BMC Bioinformatics (BMC Bioinformatics) |
| Publisher |
BioMed Central |
| ISSN |
1471-2105 |
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| Audience : |
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internationale |
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| date de publication : |
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03/10/2012 |
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date de publication
électronique : |
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03/10/2012 |
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| volume : |
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13 |
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| numéro : |
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1 |
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| page, identifiant, ... : |
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254 |
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| mots-clés auteur : |
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LSDB – Variation database curation – Data collection – Distribution |
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| Projet Européen : |
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| 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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