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MOLGENIS catalogue


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


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
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.


10 known installations.



  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-2013-002577

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  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.

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Correspondence to Morris Swertz.

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Swertz, M., van Enckevort, D. & Pang, C. MOLGENIS catalogue. J Clin Bioinform 5 (Suppl 1), S8 (2015).

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