title: MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.
abstract: 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.
  
  
  
  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.
  
  
  
  Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect
  
  
  
  : m.a.swertz@rug.nl
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: 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.
authors.forename: Chao
authors.initials: C
authors.lastname: Pang
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: David
authors.initials: D
authors.lastname: van Enckevort
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: de Haan
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Fleur
authors.initials: F
authors.lastname: Kelpin
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Jetten
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Dennis
authors.initials: D
authors.lastname: Hendriksen
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Tommy
authors.initials: T
authors.lastname: de Boer
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Bart
authors.initials: B
authors.lastname: Charbon
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: Erwin
authors.initials: E
authors.lastname: Winder
authors.affiliation: Department of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
authors.forename: K Joeri
authors.initials: KJ
authors.lastname: van der Velde
authors.affiliation: Research Institute of the McGill University Health Centre and Department of Medicine, McGill University, Montreal, Canada.
authors.forename: Dany
authors.initials: D
authors.lastname: Doiron
authors.affiliation: Research Institute of the McGill University Health Centre and Department of Medicine, McGill University, Montreal, Canada.
authors.forename: Isabel
authors.initials: I
authors.lastname: Fortier
authors.affiliation: Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
authors.forename: Hans
authors.initials: H
authors.lastname: Hillege
authors.affiliation: 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.
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
mesh_terms: D000465:Algorithms; D064229:Biological Ontologies; D018070:Biological Specimen Banks; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D010641:Phenotype; D012984:Software