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MOLGENIS/OMX for multi-omics and personalized medicine
Journal of Clinical Bioinformatics volume 5, Article number: S5 (2015)
Characterisation
Tool, genomics, personalized medicine, meta-data, data, annotation, integration, visualization, open source/free.
Description
MOLGENIS/omx [1] is a generic toolbox for multi-omics and personalized medicine studies such as EU-Panacea, EU-BioSHaRE, EU-BioMedBridges, NL-String of Pearls, and CTMM/Triumph. OMX comes with a simple Excel format to upload data; a powerful data explorer to find and filter data; a genome browser; an R statistical programming interface for bioinformaticians and integrated annotation tools for Chembl, Ensembl, OMIM, etc. Increasingly bigger datasets are required for epidemiological and genetic analysis and hence, it has ‘big data’ stores connected using VCF and Elastic searches. MOLGENIS/omx gave rise to a variety of web applications in the life science domain, including omics data warehouses, patient mutation registries, and clinical data integration platforms. For example, the WormQTLHD database [2] contains over 60 omics data sets contributed by the international C. elegans research community. Patient registries such as those developed for MVID [3], Dystrophic EB, and CHARGE syndrome enable clinicians to enter data about patient phenotypes and causal mutations. MOLGENIS/omx most recent application is to facilitate interpretation of the massive amounts of genomics data, including eQTL pathogenicity predictions, and/or clinical interpretation of NGS data in research consortia and clinical labs.
Status of development
Version 1.2.0.
Users
10 known installations.
Links
http://github.com/molgenis/molgenis, http://www.molgenis.org
MOLGENIS/omx genome browser in the COL7A mutation database.
References
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, et al: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics. 2010, 11 (Suppl 12): S12-10.1186/1471-2105-11-S12-S12.
Van der Velde KJ, de Haan M, Zych K, Arends D, Snoek LB, Kammenga JE, et al: WormQTLHD - a web database for linking human disease to natural variation data in C. elegans. Nucleic Acids Res. 2014, 42 (Database issue): D794-D801.
Van der Velde KJ, Dhekne HS, Swertz M, Sirigu S, Ropars V, Vinke PC, van Ijzendoorn SCD, et al: An overview and online registry of microvillus inclusion disease patients and their MYO5B mutations. Human Mutation. 2013, 34 (12): 1597-1605. 10.1002/humu.22440.
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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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Swertz, M., van der Velde, K.J. MOLGENIS/OMX for multi-omics and personalized medicine. J Clin Bioinform 5 (Suppl 1), S5 (2015). https://doi.org/10.1186/2043-9113-5-S1-S5
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DOI: https://doi.org/10.1186/2043-9113-5-S1-S5
Keywords
- Personalized Medicine
- Data Warehouse
- Annotation Tool
- Omics Data
- Science Domain