Article (Scientific journals)
Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
Barbosa-Silva, Adriano; Bratfalean, Dorina; Gu, Wei et al.
2018In Bioinformatics, p. 809
Peer reviewed
 

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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 center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Life sciences: Multidisciplinary, general & others
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)
More authors (4 more) Less
External co-authors :
yes
Language :
English
Title :
Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
Publication date :
2018
Journal title :
Bioinformatics
Pages :
bty809
Peer reviewed :
Peer reviewed
Focus Area :
Systems Biomedicine
European Projects :
FP7 - 115446 - ETRIKS - Delivering European Translational Information & Knowledge Management Services
Name of the research project :
R-AGR-0454 - eTRIKS (20121001-20180930) - SCHNEIDER Reinhard
Funders :
CE - Commission Européenne [BE]
Available on ORBilu :
since 26 September 2018

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