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MOLGENIS catalogue
Journal of Clinical Bioinformatics volume 5, Article number: S8 (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:
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1)
Biobank/study descriptions using custom or MIABIS standard of BBMRI-ERIC format;
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2)
Data schema/data dictionary of data elements;
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3)
Aggregate data/sample availability counts and;
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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).
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.
References
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-2013-002577
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.
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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 Enckevort, D. & Pang, C. MOLGENIS catalogue. J Clin Bioinform 5 (Suppl 1), S8 (2015). https://doi.org/10.1186/2043-9113-5-S1-S8
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DOI: https://doi.org/10.1186/2043-9113-5-S1-S8