title: VarioML framework for comprehensive variation data representation and exchange.
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 (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.
  
  
  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.
authors.affiliation: Institute for Molecular Medicine Finland-FIMM, University of Helsinki, Helsinki, Finland. juha.muilu@helsinki.fi
authors.forename: Myles
authors.initials: M
authors.lastname: Byrne
authors.forename: Ivo Fac
authors.initials: IF
authors.lastname: Fokkema
authors.forename: Owen
authors.initials: O
authors.lastname: Lancaster
authors.forename: Tomasz
authors.initials: T
authors.lastname: Adamusiak
authors.forename: Anni
authors.initials: A
authors.lastname: Ahonen-Bishopp
authors.forename: David
authors.initials: D
authors.lastname: Atlan
authors.forename: Christophe
authors.initials: C
authors.lastname: Béroud
authors.forename: Michael
authors.initials: M
authors.lastname: Cornell
authors.forename: Raymond
authors.initials: R
authors.lastname: Dalgleish
authors.forename: Andrew
authors.initials: A
authors.lastname: Devereau
authors.forename: George P
authors.initials: GP
authors.lastname: Patrinos
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
authors.forename: Peter Em
authors.initials: PE
authors.lastname: Taschner
authors.forename: Gudmundur A
authors.initials: GA
authors.lastname: Thorisson
authors.forename: Mauno
authors.initials: M
authors.lastname: Vihinen
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Brookes
authors.forename: Juha
authors.initials: J
authors.lastname: Muilu
mesh_terms: D003199:Computer Systems; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D033181:Information Dissemination / Q000379:methods*