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Barbosa-Silva A, Bratfalean D, Gu W, Satagopam V, Houston P, Becnel LB, Eifes S, Richard F, Tielmann A, Herzinger S, Rege K, Balling R, Peeters P, Schneider R. Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART. Bioinformatics 2019; 35:1562-1565. [PMID: 30256906 PMCID: PMC6499239 DOI: 10.1093/bioinformatics/bty809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 07/30/2018] [Accepted: 09/25/2018] [Indexed: 11/13/2022] Open
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 eTRIKS—Master Tree branch, where the discussed examples can be visualized.
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Affiliation(s)
- Adriano Barbosa-Silva
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg.,Department of Clinical Pharmacology, Centre for Translational Bioinformatics, William Harvey Research, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M6BQ, UK
| | - Dorina Bratfalean
- CDISC, Clinical Data Interchange Standards Consortium and CDISC EU Foundation, Saint-Louis, Alsace, France
| | - Wei Gu
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg
| | - Venkata Satagopam
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg
| | - Paul Houston
- CDISC, Clinical Data Interchange Standards Consortium and CDISC EU Foundation, Saint-Louis, Alsace, France
| | - Lauren B Becnel
- CDISC, Clinical Data Interchange Standards Consortium and CDISC EU Foundation, Saint-Louis, Alsace, France
| | - Serge Eifes
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg.,Information Technology for Translational Medicine (ITTM) S.A, Esch/Belval, Luxembourg
| | - Fabien Richard
- Centre National de la Recherche Scientifique (CNRS), Lyon, Auvergne-Rhône-Alpes, France
| | - Andreas Tielmann
- Department of Research and Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Sascha Herzinger
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg
| | - Kavita Rege
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg
| | - Rudi Balling
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg
| | | | - Reinhard Schneider
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg
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