VarioML framework for comprehensive variation data representation and exchange
<p>Abstract</p> <p>Background</p> <p>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 pro...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-10-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://www.biomedcentral.com/1471-2105/13/254 |
| _version_ | 1818212470565634048 |
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| author | Byrne Myles Fokkema Ivo FAC Lancaster Owen Adamusiak Tomasz Ahonen-Bishopp Anni Atlan David Béroud Christophe Cornell Michael Dalgleish Raymond Devereau Andrew Patrinos George P Swertz Morris A Taschner Peter EM Thorisson Gudmundur A Vihinen Mauno Brookes Anthony J Muilu Juha |
| author_facet | Byrne Myles Fokkema Ivo FAC Lancaster Owen Adamusiak Tomasz Ahonen-Bishopp Anni Atlan David Béroud Christophe Cornell Michael Dalgleish Raymond Devereau Andrew Patrinos George P Swertz Morris A Taschner Peter EM Thorisson Gudmundur A Vihinen Mauno Brookes Anthony J Muilu Juha |
| author_sort | Byrne Myles |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 (LSDBs) 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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-12T05:48:54Z |
| format | Article |
| id | doaj.art-ef3d377fc28f4c09a1c5a1aca6db1776 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-12T05:48:54Z |
| publishDate | 2012-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ef3d377fc28f4c09a1c5a1aca6db17762022-12-22T00:35:44ZengBMCBMC Bioinformatics1471-21052012-10-0113125410.1186/1471-2105-13-254VarioML framework for comprehensive variation data representation and exchangeByrne MylesFokkema Ivo FACLancaster OwenAdamusiak TomaszAhonen-Bishopp AnniAtlan DavidBéroud ChristopheCornell MichaelDalgleish RaymondDevereau AndrewPatrinos George PSwertz Morris ATaschner Peter EMThorisson Gudmundur AVihinen MaunoBrookes Anthony JMuilu Juha<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 (LSDBs) 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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/13/254LSDBVariation database curationData collectionDistribution |
| spellingShingle | Byrne Myles Fokkema Ivo FAC Lancaster Owen Adamusiak Tomasz Ahonen-Bishopp Anni Atlan David Béroud Christophe Cornell Michael Dalgleish Raymond Devereau Andrew Patrinos George P Swertz Morris A Taschner Peter EM Thorisson Gudmundur A Vihinen Mauno Brookes Anthony J Muilu Juha VarioML framework for comprehensive variation data representation and exchange BMC Bioinformatics LSDB Variation database curation Data collection Distribution |
| title | VarioML framework for comprehensive variation data representation and exchange |
| title_full | VarioML framework for comprehensive variation data representation and exchange |
| title_fullStr | VarioML framework for comprehensive variation data representation and exchange |
| title_full_unstemmed | VarioML framework for comprehensive variation data representation and exchange |
| title_short | VarioML framework for comprehensive variation data representation and exchange |
| title_sort | varioml framework for comprehensive variation data representation and exchange |
| topic | LSDB Variation database curation Data collection Distribution |
| url | http://www.biomedcentral.com/1471-2105/13/254 |
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