The Portuguese ELIXIR Node has been testing and providing feedback for the Local EGA and Beacon v2 repositories, being developed by ELIXIR Spain, at the Centre for Genomic Regulation (CRG).
Following these efforts, three ELIXIR Nodes, Portugal, Spain, and EMBL-EBI, joined to create recommendations and tutorials for other countries wishing to create a Local EGA node and Beacon, based on experience and lessons learned. In addition, outreach activities to raise awareness within the health sector and among citizens will be carried out.
The project started in October 2022 and will include several Zoom work sessions, a visit from the CRG team to Lisbon for the deployment of the systems, and a visit of the CRG and EMBL-EBI team to deliver a Workshop for the Portuguese Health and Life Sciences research community.
The European Genome-Phenome Archive (EGA) is a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. However, since the establishment of the General Data Protection Regulation (GDPR), the submission of sensitive (human) data has been hampered. The solution for this is a Federated EGA, where the sensitive data stays in local nodes of EGA and will serve as a permanent archive that will archive several levels of data, including the raw data, as well as the genotype calls provided by the submitters.
Beacon is an API (sometimes extended with a user interface) that allows for data discovery of genomic variants and phenoclinic data. Version 2 of the Beacon protocol has been accepted as GA4GH standard in Spring 2022 and brings many new query possibilities, including metadata filters, and facilitates access to the data owners.
