Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART

Barbosa-Silva, Adriano; Bratfalean, Dorina; Gu, Wei; Satagopam, Venkata; Houston, Paul; Becnel, Lauren B.; Eifes, Serge; Richard, Fabien; Tielmann, Andreas; Herzinger, Sascha; Rege, Kavita; Balling, Rudi; Peeters, Paul; Schneider, Reinhard

doi:10.1093/bioinformatics/bty809

Reference : Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART


	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Multidisciplinary, general & others
	Focus Areas :	Systems Biomedicine
	To cite this reference:	http://hdl.handle.net/10993/36683

Title :	Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
Language :	English
Author, co-author :	Barbosa-Silva, Adriano [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)]
	Bratfalean, Dorina [> >]
	Gu, Wei [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Satagopam, Venkata [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Houston, Paul [> >]
	Becnel, Lauren B. [> >]
	Eifes, Serge [> >]
	Richard, Fabien [> >]
	Tielmann, Andreas [> >]
	Herzinger, Sascha [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Rege, Kavita [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Balling, Rudi [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Peeters, Paul [> >]
	Schneider, Reinhard [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Publication date :	2018
Journal title :	Bioinformatics
Pages :	bty809
Peer reviewed :	Yes
Audience :	International
Abstract :	[en] Motivation Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC SDTM clinical data standard into the tranSMART i2b2 via a guiding master ontology tree positively impacts and supports the efficacy of data sharing, visualization and exploration across datasets. Results We present here a schema for the organization of SDTM variables into the tranSMART i2b2 tree along with a script and test dataset to exemplify the mapping strategy. The eTRIKS master tree concept is demonstrated by making use of fictitious data generated for four patients, including 16 SDTM clinical domains. We describe how the usage of correct visit names and data labels can help to integrate multiple readouts per patient and avoid ETL crashes when running a tranSMART loading routine. Availability The eTRIKS Master Tree package and test datasets are publicly available at https://doi.org/10.5281/zenodo.1009098 and a functional demo installation at https://public.etriks.org/transmart/datasetExplorer/ under eTRIKS - Master Tree branch, where the discussed examples can be visualized.
Research centres :	Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Funders :	European Commission - EC
Name of the research project :	R-AGR-0454 > eTRIKS > 01/10/2012 - 30/09/2017 > SCHNEIDER Reinhard
Target :	Researchers ; Professionals
Permalink :	http://hdl.handle.net/10993/36683
DOI :	10.1093/bioinformatics/bty809
Other URL :	http://dx.doi.org/10.1093/bioinformatics/bty809
Framework Programme / European Project :	FP7 ; 115446 - ETRIKS - Delivering European Translational Information & Knowledge Management Services

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