Abstract
BackgroundFor large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential for the successful collection, organization and analysis of the resulting data. Research consortia are attempting ever more ambitious science to better understand disease, by leveraging technologies such as whole genome sequencing, proteomics, patient-derived biological models and computer-based systems biology simulations.ResultsThe IMI eTRIKS consortium is charged with the task of developing an integrated knowledge management platform capable of supporting the complexity of the data generated by such research programmes. In this paper, using the example of the OncoTrack consortium, we describe a typical use case in translational medicine. 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 tumour models. The high dimensional (omics) data from the molecular analyses of the corresponding biological materials were linked to these collections, so that users could browse and analyse these to derive candidate biomarkers.ConclusionsIn all these steps, data mapping, linking and preparation are handled automatically by the tranSMART integration platform. Therefore, researchers without specialist data handling skills can focus directly on the scientific questions, without spending undue effort on processing the data and data integration, which are otherwise a burden and the most time-consuming part of translational research data analysis.
Highlights
We present the broad overall systems architecture developed by the eTRIKS consortium to accommodate the data management requirements of translational research consortia, using the Innovative Medicines Initiative (IMI) OncoTrack project as a use case
Results visualization High Dimensional and Omics Exploration (HiDome) is a novel functionality for tranSMART that was developed through eTRIKS Labs [10]
Oncotrack TranSMART The current Oncotrack TranSMART deployed to the consortium is based on the eTRIKS distribution of tranSMART 16.1
Summary
The data are not just made available in curated form, but are made accessible This is achieved by the use of flexible user interfaces, combined with analytical and visualization tools that can be used by all stakeholders in the consortium and not just those with the specialist data handling skills such as bioinformaticians and statisticians. A consortium that provides a data coordination capability accelerates the work of the specialist data scientist who can access the raw data from a single location for specialist analysis If this data coordination capability includes a knowledge management technology, this can empower the wider community of scientists who are able to browse and generate hypotheses from all of the data in an accessible format
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