title: Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
abstract: Genetic and epidemiological research increasingly employs large collections of phenotypic and molecular observation data from high quality human and model organism samples. Standardization efforts have produced a few simple formats for exchange of these various data, but a lightweight and convenient data representation scheme for all data modalities does not exist, hindering successful data integration, such as assignment of mouse models to orphan diseases and phenotypic clustering for pathways. We report a unified system to integrate and compare observation data across experimental projects, disease databases, and clinical biobanks. The core object model (Observ-OM) comprises only four basic concepts to represent any kind of observation: Targets, Features, Protocols (and their Applications), and Values. An easy-to-use file format (Observ-TAB) employs Excel to represent individual and aggregate data in straightforward spreadsheets. The systems have been tested successfully on human biobank, genome-wide association studies, quantitative trait loci, model organism, and patient registry data using the MOLGENIS platform to quickly setup custom data portals. Our system will dramatically lower the barrier for future data sharing and facilitate integrated search across panels and species. All models, formats, documentation, and software are available for free and open source (LGPLv3) at http://www.observ-om.org.
authors.affiliation: EU-GEN2PHEN, and European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Adamusiak
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.forename: Juha
authors.initials: J
authors.lastname: Muilu
authors.forename: Erik
authors.initials: E
authors.lastname: Roos
authors.forename: Kasper Joeri
authors.initials: KJ
authors.lastname: van der Velde
authors.forename: Gudmundur A
authors.initials: GA
authors.lastname: Thorisson
authors.forename: Myles
authors.initials: M
authors.lastname: Byrne
authors.forename: Chao
authors.initials: C
authors.lastname: Pang
authors.forename: Sirisha
authors.initials: S
authors.lastname: Gollapudi
authors.forename: Vincent
authors.initials: V
authors.lastname: Ferretti
authors.forename: Hans
authors.initials: H
authors.lastname: Hillege
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Brookes
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
mesh_terms: D000818:Animals; D003196:Computer Graphics; D030541:Databases, Genetic; D016108:Epidermolysis Bullosa Dystrophica / Q000235:genetics; D056726:Genetic Association Studies; D006801:Humans; D033181:Information Dissemination / Q000379:methods*; D019451:Information Management; D008490:Medical Informatics; D051379:Mice; D010641:Phenotype; D040641:Quantitative Trait Loci