These authors contributed equally to this work.
Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information†
Article first published online: 4 APR 2012
© 2012 Wiley Periodicals, Inc.
Special Issue: Deep Phenotyping for Precision Medicine
Volume 33, Issue 5, pages 867–873, May 2012
How to Cite
Adamusiak, T., Parkinson, H., Muilu, J., Roos, E., van der Velde, K. J., Thorisson, G. A., Byrne, M., Pang, C., Gollapudi, S., Ferretti, V., Hillege, H., Brookes, A. J. and Swertz, M. A. (2012), Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information. Hum. Mutat., 33: 867–873. doi: 10.1002/humu.22070
For the Deep Phenotyping Special Issue
- Issue published online: 13 APR 2012
- Article first published online: 4 APR 2012
- Accepted manuscript online: 13 MAR 2012 12:31PM EST
- Manuscript Accepted: 22 FEB 2012
- Manuscript Received: 21 DEC 2011
- GEN2PHEN, BioSHaRE, and PANACEA (European Commission). Grant Number: FP7-HEALTH contracts 200754, 261433, and 222936
- The BBMRI-NL dynamic bioinformatics infrastructure rainbow project (BBMRI-NL RP-2)
- The BBMRI-FI (Academy of Finland/Biomedinfra), NBIC BioAssist/Biobanking, and the NWO (Rubicon Grant 825.09.008)
- data model;
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. Hum Mutat 33:867–873, 2012. © 2012 Wiley Periodicals, Inc.