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Article 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937195 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btw155 | DOI Listing |
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