Volume 5 Supplement 1

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

Open Access

MOLGENIS catalogue

Journal of Clinical Bioinformatics20155(Suppl 1):S8

https://doi.org/10.1186/2043-9113-5-S1-S8

Published: 22 May 2015

Characterisation

Tool, biobanking, meta-data, data, miabis, open source.

Description

MOLGENIS/catalogue is a generic toolbox for building biobank and study catalogues and is used in BBMRI-NL, EU-BioSHaRE, EU-BioMedBridges, LifeLines, CTMM/TraIT, Durrer Center, PALGA NL pathology network. The catalogue can host four levels of information:
  1. 1)

    Biobank/study descriptions using custom or MIABIS standard of BBMRI-ERIC format;

     
  2. 2)

    Data schema/data dictionary of data elements;

     
  3. 3)

    Aggregate data/sample availability counts and;

     
  4. 4)

    Individual level data ready for analysis.

     
Increasingly bigger datasets are required for epidemiological and genetic analysis; hence it has become important to enable pooling of data from multiple biobanks. Therefore, the catalogue also comes with BiobankConnect, a tool to rapidly match data elements across studies and biobanks based on lexical matching and ontologies [1]. MOLGENIS/catalogue is build on the open source MOLGENIS platform [2] and offers pre-build components that allow users to upload data in a simple Excel format and supports any data model through a meta-data definition in the Excel file; to visualize the data in aggregated or tabular form; to share securely data through a comprehensive security model and to integrate data from different domains (Figure 1).
Figure 1

MOLGENIS/catalogue data explorer for the DeCoDe study. Users can filter, aggregate and drill down on available data.

Status of development

Stable/production ready; version 1.2.0.

Users

10 known installations.

Links

Authors’ Affiliations

(1)
Department of Genetics, University Medical Center Groningen, University of Groningen
(2)
Department of Epidemiology, University of Groningen, University Medical Center Groningen

References

  1. Pang C, Hendriksen D, Dijkstra M, van der Velde KJ, Kuiper J, Hillege H, Swertz MA: BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. J Am Med Inform Assoc. 2014, epub ahead of print. doi: 10.1136/amiajnl-2013-002577Google Scholar
  2. 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

Copyright

© Swertz et al; 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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