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Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART

Adriano Barbosa-Silva, Dorina Bratfalean, Wei Gu, Venkata Satagopam, Paul Houston, Lauren B Becnel, Serge Eifes, Fabien Richard, Andreas Tielmann, Sascha Herzinger, Kavita Rege, Rudi Balling (+3 others)
2018 Bioinformatics  
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  ...  The eTRIKS master tree concept is demonstrated by making use of fictitious data generated for four patients, including 16 SDTM clinical domains.  ...  Acknowledgements Experiments presented in this paper were carried out using the HPC facilities of University of Luxembourg (  ... 
doi:10.1093/bioinformatics/bty809 pmid:30256906 pmcid:PMC6499239 fatcat:cyrfs5fanjdpdfj4jqvnssf4ey

Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium

Wei Gu, Reha Yildirimman, Emmanuel Van der Stuyft, Denny Verbeeck, Sascha Herzinger, Venkata Satagopam, Adriano Barbosa-Silva, Reinhard Schneider, Bodo Lange, Hans Lehrach, Yike Guo, David Henderson (+1 others)
2019 BMC Bioinformatics  
for the successful collection, organization and analysis of the resulting data.  ...  The tranSMART knowledge management platform was implemented to support data from observational clinical cohorts, drug response data from cell culture models and drug response data from mouse xenograft  ...  Acknowledgements We thank all participants from the OncoTrack and eTRIKS consortia for their contributions to the projects.  ... 
doi:10.1186/s12859-019-2748-y pmid:30935364 pmcid:PMC6444691 fatcat:bok54rxpivf4tkdzzgvydrpjly

Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases

Venkata Satagopam, Wei Gu, Serge Eifes, Piotr Gawron, Marek Ostaszewski, Stephan Gebel, Adriano Barbosa-Silva, Rudi Balling, Reinhard Schneider
2016 Big Data  
In this article, we present an integrated workflow for exploring, analysis, and interpretation of translational medicine data in the context of human health.  ...  The capabilities of tranSMART enable a flexible filtering of multidimensional integrated data sets to create subsets suitable for downstream processing.  ...  This work has received support from the EU/EFPIA Innovative Medicines Initiative Joint Undertaking AETIONOMY and eTRIKS grants and LCSB, University of Luxembourg.  ... 
doi:10.1089/big.2015.0057 pmid:27441714 pmcid:PMC4932659 fatcat:n7fcnszchrhk5of3kvkmvvjbty

Corbel Robust Data Upload Procedures For Biosample Data And Molecular Profiling Data

Jan-Willem Boiten, Mariska Bierkens, Matthias Hansson, Stefan Klein, Sjaak Peelen
2017 Zenodo  
The present document describes a detailed set of guidelines how to execute those data curation and modeling steps for each of the supported data types in tranSMART, cBioportal, and XNAT.  ...  The core of the CORBEL common IT framework for genomics and imaging studies in biomarker research consists of the tranSMART (data integration and browsing platform), cBioportal (patient-level genomics  ...  Data integration platform: tranSMART tranSMART is a data integration, sharing, and analysis platform for clinical and translational research.  ... 
doi:10.5281/zenodo.886507 fatcat:zrugjipjofhzresgq6ml5nt77u

Open Source Software Sustainability Models: Initial White Paper from the Informatics Technology for Cancer Research Sustainability and Industry Partnership Work Group [article]

Y. Ye, R. D. Boyce, M.K. Davis, K. Elliston, C. Davatzikos, A. Fedorov, J. C. Fillion-Robin, I. Foster, J. Gilbertson, M. Heiskanen, J. Klemm, A. Lasso (+10 others)
2020 arXiv   pre-print
This article reviews existing sustainability models and describes ten OSS use cases disseminated by the SIP-WG and others, and highlights five essential attributes (alignment with unmet scientific needs  ...  The Sustainability and Industry Partnership Work Group (SIP-WG) is a part of the National Cancer Institute Informatics Technology for Cancer Research (ITCR) program.  ...  Red Hat provides storage, operating system platforms, middleware, applications, management products, and support, training, and consulting services.  ... 
arXiv:1912.12371v2 fatcat:p6he4khh5bgmbfjdcyl6dx5t6q

eTRIKS analytical environment: a practical platform for medical big data analysis

Axel Oehmichen, Yi-Ke Guo
We will present the use of location data in the context of public health research, the work done in the context of data privacy for location data and the ex [...]  ...  leverage complex molecular and clinical data from that variety of large-scale heterogeneous data sources.  ...  Chapter 6 Analytics Developed using the eTRIKS Analytical Environment Analytics for tranSMART To illustrate how the eTRIKS Analytical Environment can be used for managing and analysing large scale translational  ... 
doi:10.25560/82541 fatcat:snbou7u3qfgm5cswvm4o4xxb4m

Immersive social visual analytics

Ahmet Bertan Kavuncu, Yi-Ke Guo
In summary, this thesis presents architecture and implementation of Data Observatory Software Framework (GDO), which is used at KPMG Data Observatory, Data Science Institute, Imperial College London; its  ...  This thesis surveyed existing software in the literature for LHRDs and identified many challenges that needed to be solved, in order to conduct visual data analytics for this objective.  ...  B. tranSMART: DSI has a eTRIKS/tranSMART visualisation application [155] for visualising data related to eTRIKS project [64] .  ... 
doi:10.25560/84842 fatcat:5tkdoqvmi5esbdyjlnv3j42ik4