Dataset Information

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

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.

SUBMITTER: Pang C

PROVIDER: S-EPMC4937195 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Pang Chao C van Enckevort David D de Haan Mark M Kelpin Fleur F Jetten Jonathan J Hendriksen Dennis D de Boer Tommy T Charbon Bart B Winder Erwin E van der Velde K Joeri KJ Doiron Dany D Fortier Isabel I Hillege Hans H Swertz Morris A MA

Bioinformatics (Oxford, England) 20160321 14

<h4>Motivation</h4>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.<h4>Results</h4>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 ontolog ...[more]

PMID: 27153686

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Dataset Information

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

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

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

Similar Datasets

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