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CORBEL Robust data upload procedures for biosample data and molecular profiling data

Boiten, Jan-Willem; Bierkens, Mariska; Hansson, Matthias; Klein, Stefan; Peelen, Sjaak

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 platform) and XNAT (image archive platform) solutions. Loading existing project data into these platforms requires some level of data curation and transformation. This is particularly true for tranSMART, which is suited to handle a wide range of data types but also requires careful data modeling of those data before loading. 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. It is partially based on previous work in the Dutch TraIT platform which was applied to the CORBEL use cases. Some practical lessons learned from those use cases, in particular the IMI APPROACH project, are given as well.

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