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ELIXIR::GA4GH: Advancing genomics through expedited data access enabled by standards and ontologies


Wednesday, 2nd September


17:00 to 20:00 (CEST)


  • Gary Saunders | ELIXIR Hub, United Kingdom
  • Melanie Courtot | EMBL-EBI, United Kingdom
  • Michael Baudis | University of Zurich, ELIXIR-CH, Switzerland
  • Tommi Nyronen | CSC, ELIXIR-FI, United Kingdom
  • Jordi Rambla | CRG, ELIXIR-ES, Spain

Invited Speakers

  • TBA


Research cohorts of hundreds of thousands of human genomes have emerged as a result of the decreasing cost of sequencing, posing a significant opportunity to advance global public health. However, major barriers to international data access have hindered effective use of the data, including: 

1) lack of data sharing mandates

2) data submission challenges

3) inadequate resources for data ingestion and storage

4) ambiguous consent language

5) lack of dataset interoperability due to disparate data models and terminologies

6) inability to address privacy issues and provide secure access management. 

The Global Alliance for Genomics and Health (GA4GH) convenes research and healthcare communities to overcome these barriers and fulfill the benefit from science as stated in the Universal Declaration of Human Rights. With input from 23 real-world genomic data initiatives, known as Driver Projects, GA4GH Work Streams so far have released 13 technical standards and 18 policies in such areas as Large Scale Genomics, Cloud, Data Use & Researcher Identity, Clinical & Phenotypic Data Capture, Discovery, Genomic Knowledge Standards, Regulatory & Ethics, and Data Security. Further items are in active development and a roadmap of additional deliverables will be rolled out during 2020. 

In 2019 ELIXIR, the distributed European infrastructure for life-science information, formed the first Strategic Partnership with GA4GH. This agreement serves as the basis for European bioinformatics and biomedical research communities to ‘speak with one voice’ directly to GA4GH leadership and to ensure that approved products can be considered “Gold Standard” in their given areas, ready to be implemented in both research and clinical settings. 

In this workshop participants will gain an understanding of how ELIXIR is working with GA4GH to generate and implement standards that can support their research and facilitate improvements to the technical resources at their local institutions and specific projects. In particular, we will present and discuss elements from our toolkit that are ready for real-world use: 

  • Data access through Passports and the Data Use Ontology
  • Phenopackets, a standard for capturing machine-readable clinical & phenotypic data
  • Beacon, a privacy-protecting web API for federated genomic data discovery
  • htsget, a standard for securely streaming genomic data
  • SchemaBlocks, an initiative to facilitate data model and code alignment across GA4GH products.

Target audience

Bioinformaticians, clinicians, and scientists with an interest in data access infrastructure. Throughout this interactive event, attendees will be able to (1) explore existing platforms built on GA4GH standards to interact with real-world data, (2) gain a high-level understanding of the requirements and steps for implementing those standards, and (3) learn how to participate in GA4GH activities.