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Integration of EGA secure data access into Galaxy.

Youri Hoogstrate1, Chao Zhang2, Alexander Senf3

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Summary

A new tool, ega_download_streamer, enables secure downloading of sensitive European Genome-phenome Archive (EGA) data into Galaxy servers. This facilitates reproducible analysis of molecular profiling data for translational medicine research.

Keywords:
EGAGalaxybioinformaticsdata managementtranslational researchworkflows

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Area of Science:

  • Bioinformatics
  • Genomics
  • Translational Medicine

Background:

  • High-throughput molecular profiling generates vast, sensitive data requiring secure management.
  • The European Genome-phenome Archive (EGA) provides secure archival and access to bio-molecular data.
  • ELIXIR's 2016 Human Data Implementation Study aimed to define requirements for secure controlled-access data management.

Purpose of the Study:

  • To develop a framework for securely downloading EGA data into a Galaxy server.
  • To enable secure, end-to-end analysis of sensitive molecular profiling data within Galaxy.
  • To enhance reproducibility of translational research involving sensitive genomic data.

Main Methods:

  • Designed a secure data management ecosystem connecting raw and interpreted data with computational workflows.
  • Developed the 'ega_download_streamer' tool for secure data transfer from EGA to Galaxy.
  • Utilized the CTMM Translational Research IT (CTMM-TraIT) infrastructure as a model.

Main Results:

  • Successfully created a framework enabling secure download of EGA data to Galaxy.
  • The 'ega_download_streamer' tool facilitates secure data processing within the Galaxy environment.
  • Demonstrated a proof-of-concept for reproducible analysis of sensitive EGA data.

Conclusions:

  • The developed framework and tool significantly improve secure data handling for translational research.
  • Enables researchers to perform complete, reproducible analyses of sensitive genomic data.
  • The 'ega_download_streamer' tool is available via the Galaxy Tool Shed for wider adoption.