Paper Info
Title
Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART.
Abstract
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 and implementation 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 eTRIKSMaster Tree branch, where the discussed examples can be visualized.
Year
DOI
Venue
2019
10.1093/bioinformatics/bty809
BIOINFORMATICS
Field
DocType
Volume
Data science,Data mining,Computer science
Journal
35
Issue
ISSN
Citations 
9
1367-4803
0
PageRank 
References 
Authors
0.34
0
14
Name
Order
Citations
PageRank
Adriano Barbosa-Silva11558.15
Dorina Bratfalean200.34
Wei Gu392.38
Venkata P Satagopam411610.76
Paul Houston58922.34
Lauren B Becnel621.75
Serge Eifes740.89
Fabien Richard800.34
Andreas Tielmann900.34
Sascha Herzinger1041.23
Kavita Rege1140.89
Rudi Balling1251.14
Paul Peeters1300.34
Reinhard Schneider1447528.53