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) Biobank/study descriptions using custom or MIABIS standard of BBMRI-ERIC format;
2) Data schema/data dictionary of data elements;
3) Aggregate data/sample availability counts and;
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
http://github.com/molgenis/molgenis, http://www.molgenis.org, https://www.dropbox.com/s/bez1r4lq5q69o9e/Swertz%20ECRIN%20Dussseldorf%20catalogue%202014_05_26.pptx.pdf.pdf
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. [DOI] [PMC free article] [PubMed]
- 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. doi: 10.1186/1471-2105-11-S12-S12. [DOI] [PMC free article] [PubMed] [Google Scholar]