Reference : Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
Systems Biomedicine
http://hdl.handle.net/10993/36683
Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
English
Barbosa-Silva, Adriano [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)]
Bratfalean, Dorina [> >]
Gu, Wei mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Satagopam, Venkata mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Houston, Paul [> >]
Becnel, Lauren B. [> >]
Eifes, Serge [> >]
Richard, Fabien [> >]
Tielmann, Andreas [> >]
Herzinger, Sascha mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Rege, Kavita mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Balling, Rudi mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Peeters, Paul [> >]
Schneider, Reinhard mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
2018
Bioinformatics
bty809
Yes
International
[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.
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
European Commission - EC
Researchers ; Professionals
http://hdl.handle.net/10993/36683
10.1093/bioinformatics/bty809
http://dx.doi.org/10.1093/bioinformatics/bty809
FP7 ; 115446 - ETRIKS - Delivering European Translational Information & Knowledge Management Services

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