Volume 5 Supplement 1

Abstracts from the 1st Clinical Research Informatics (CRI) Solutions Day 2014

Open Access

MOLGENIS/OMX for multi-omics and personalized medicine

Journal of Clinical Bioinformatics20155(Suppl 1):S5

https://doi.org/10.1186/2043-9113-5-S1-S5

Published: 22 May 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
Figure 1

MOLGENIS/omx genome browser in the COL7A mutation database.

Authors’ Affiliations

(1)
Genomics Coordination Center, Department of Genetics, University Medical Center Groningen

References

  1. 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.PubMed CentralView ArticlePubMedGoogle Scholar
  2. 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.PubMed CentralView ArticlePubMedGoogle Scholar
  3. 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.View ArticlePubMedGoogle Scholar

Copyright

© Swertz and van der Velde; licensee BioMed Central Ltd. 2015

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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