Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART
| Autor: | Kavita Rege, Andreas Tielmann, Rudi Balling, Sascha Herzinger, Dorina Bratfalean, Venkata P. Satagopam, Reinhard Schneider, Paul Houston, Adriano Barbosa-Silva, Paul Peeters, Fabien Richard, Serge Eifes, Wei Gu, Lauren B. Becnel |
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| Přispěvatelé: | European Commission - EC [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center] |
| Rok vydání: | 2018 |
| Předmět: |
Statistics and Probability
Standardization Computer science Databases and Ontologies Information Storage and Retrieval Multidisciplinary general & others [F99] [Life sciences] computer.software_genre Biochemistry Multidisciplinaire généralités & autres [F99] [Sciences du vivant] 03 medical and health sciences Schema (psychology) Humans Molecular Biology 030304 developmental biology 0303 health sciences Data collection Information retrieval Information Dissemination Data Collection 030302 biochemistry & molecular biology Original Papers Data Accuracy Computer Science Applications Visualization Data sharing Data Standard Computational Mathematics Computational Theory and Mathematics computer Data integration |
| Zdroj: | Bioinformatics Bioinformatics, 809. (2018). |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/bty809 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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