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Bioinformatics. 2016 Jul 15;32(14):2176-83. doi: 10.1093/bioinformatics/btw155. Epub 2016 Mar 21.

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.

Author information

1
Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
2
Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
3
Research Institute of the McGill University Health Centre and Department of Medicine, McGill University, Montreal, Canada.
4
Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

Abstract

MOTIVATION:

While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration.

RESULTS:

To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data.

AVAILABILITY AND IMPLEMENTATION:

Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect

CONTACT:

: m.a.swertz@rug.nl

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27153686
PMCID:
PMC4937195
DOI:
10.1093/bioinformatics/btw155
[Indexed for MEDLINE]
Free PMC Article

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