Evidence map›Paper›PMID 27153686›Full record

ArticleBioinformatics (Oxford, England)2016

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

Chao Pang, David van Enckevort, Mark de Haan, Fleur Kelpin, Jonathan Jetten, Dennis Hendriksen, Tommy de Boer, Bart Charbon, Erwin Winder, K Joeri van der Velde and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Chao PangDepartment 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.
David van EnckevortDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Mark de HaanDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Fleur KelpinDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Jonathan JettenDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Dennis HendriksenDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Tommy de BoerDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Bart CharbonDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Erwin WinderDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
K Joeri van der VeldeDepartment of Genetics, University Medical Center Groningen, Genomics Coordination Center, University of Groningen, Groningen, The Netherlands.
Dany DoironResearch Institute of the McGill University Health Centre and Department of Medicine, McGill University, Montreal, Canada.
Isabel FortierResearch Institute of the McGill University Health Centre and Department of Medicine, McGill University, Montreal, Canada.
Hans HillegeDepartment of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Morris A SwertzDepartment 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.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

motivationWhile 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.

resultsTo 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.

Indexed as

Biological Specimen BanksPhenotypeSoftwareAlgorithmsBiological OntologiesComputational BiologyHumans

Identifiers

PMID27153686
PMCPMC4937195

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.