Abstract
High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies. Secure access controlled systems are needed to manage, store, transfer and distribute these data due to its personally identifiable nature. The European Genome-phenome Archive (EGA) was created to facilitate access and management to long-term archival of bio-molecular data. Each data provider is responsible for ensuring a Data Access Committee is in place to grant access to data stored in the EGA. Moreover, the transfer of data during upload and download is encrypted. ELIXIR, a European research infrastructure for life-science data, initiated a project (2016 Human Data Implementation Study) to understand and document the ELIXIR requirements for secure management of controlled-access data. As part of this project, a full ecosystem was designed to connect archived raw experimental molecular profiling data with interpreted data and the computational workflows, using the CTMM Translational Research IT (CTMM-TraIT) infrastructure http://www.ctmm-trait.nl as an example. Here we present the first outcomes of this project, a framework to enable the download of EGA data to a Galaxy server in a secure way. Galaxy provides an intuitive user interface for molecular biologists and bioinformaticians to run and design data analysis workflows. More specifically, we developed a tool -- ega_download_streamer - that can download data securely from EGA into a Galaxy server, which can subsequently be further processed. This tool will allow a user within the browser to run an entire analysis containing sensitive data from EGA, and to make this analysis available for other researchers in a reproducible manner, as shown with a proof of concept study. The tool ega_download_streamer is available in the Galaxy tool shed: https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer.
Highlights
With the advent of high-resolution and high-throughput experimental platforms the field of biomedical research has become more complex, with major shifts in data diversity and dimensions
Solutions for the increasing demand of data processing, storage and workflow management are required for translational research
Use case As a proof of concept we show how the Galaxy European Genome-phenome Archive (EGA) download streamer may be used in a workflow to detect fusion genes from RNA-seq data
Summary
With the advent of high-resolution and high-throughput experimental platforms the field of biomedical research has become more complex, with major shifts in data diversity and dimensions. Solutions for the increasing demand of data processing, storage and workflow management are required for translational research. Due to the privacy issues related to the clinical nature of translational research and personal footprints in molecular data, there is a need for a secure framework to store and analyse data. The aim of CTMM Translational Research IT (CTMM-TraIT) project is to provide a multidomain IT-infrastructure as an end-to-end solution where researchers can capture, process, and share their study data. CTMM-TraIT makes use of large community-driven open source software including tranSMART1–3 and Galaxy[4,5]. In a collaboration between ELIXIR, CTMM-TraIT and European Genomephenome Archive(EGA) a full ecosystem was designed, as shown, to connect the storage of raw molecular profiling data with processed data and the computational workflows In a collaboration between ELIXIR, CTMM-TraIT and European Genomephenome Archive(EGA) a full ecosystem was designed, as shown in Figure 1, to connect the storage of raw molecular profiling data with processed data and the computational workflows
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