Large scale genomics sequencing initiatives around the globe are beginning to generate tens of millions of genome sequences for research and healthcare purposes. These data hold great promise for the future of human health and medicine—but only if they can be responsibly shared across traditional boundaries.
EMBL-EBI is helping to enable this global ecosystem of genomics data and services by participating in GA4GH, the international standards body for genomics. The co-release of the 2020 GA4GH Connection Demos represents the first time this community has shown real-world interoperability using standards implemented at disparate institutions to search for, access, and analyse genomics data from around the world.
The three 2020 Connection Demos are:
- Horizontal Connection Demo: To emphasize progress of GA4GH in the real world, these demos show reproducibility of analyses run in different environments and portability across analytics workspaces. A GWAS analysis of 1000 Genomes data is replicated across implementations of GA4GH APIs hosted by several organisations—including DNAstack, Terra (Broad Institute/Verily), ELIXIR, and Seven Bridges—implementing GA4GH APIs.
- Vertical Connection Demo: Demonstrating the value of GA4GH standards used in combination, DNAstack has integrated multiple standards — Workflow Execution Service (WES), Data Repository Service (DRS), Passports, and Search — to enable discovery, access, and analysis of controlled data. Using real-world implementations of these open standards, this demo highlights how users can search for genomic data of interest and pass the results to inputs of a bioinformatics workflow. The demo includes data hosted on two different cloud computing platforms, Google Cloud Platform and Amazon Web Services.
- Cross Platform Connection Demo: Finally, driven by researcher needs in pediatric cancer and other diseases, the FASP team has begun work to explore how a researcher might combine the GA4GH components provided by many different institutions to aggregate data for analysis. This demonstration uses implementations of multiple GA4GH standards and data from multiple GA4GH Driver Projects and organisations—including several of the US National Institutes of Health, the European Genome-phenome Archive (EGA), Seven Bridges, and Google. Additionally, this initiative provides a social and technical framework for engaging additional data and tool providers around the globe in 2021.
EMBL-EBI worked closely with ELIXIR and GA4GH collaborators to help coordinate the elements of the Horizontal Connection Demo. “With this demo, we're showing how a single GWAS workflow can fetch data, tools, and execute in different systems to produce the same results. We’re hoping this will encourage repositories and workflow systems to adopt GA4GH standards, saving researchers time and effort and enabling federated analysis.” explains Justin Clark-Casey, European Open Science Cloud Programme Manager at EMBL-EBI.
“The Connection Demos are an enormous success for the members of the GA4GH Work Streams, who have collectively dedicated thousands of hours over the last three years toward standards development,” says Ewan Birney, Deputy Director General of the European Molecular Biology Laboratory (EMBL), Director of EMBL’s European Bioinformatics Institute (EMBL-EBI), and Chair of GA4GH. “The demos show how this community’s work will enable interoperability across the genomics endeavour.”
Find out more about the GA4GH Connection demos on the GA4GH website.
Image credit: Global Alliance for Genomics and Health (GA4GH)