The European Genome-phenome Archive (EGA) is a repository for all types of sequence and genotype
experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive
that will archive several levels of data including the raw data (which could, for example, be re-analysed in the
future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting
data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy
and operate Local EGA instances. Beacon is an API (sometimes extended with a user interface) that allows for
data discovery of genomic and phenoclinic data. The version 2 (v2) of the Beacon protocol has been accepted as
GA4GH standard in Spring 2022 and brings many new query possibilities including metadata filters, and facilitates
the access to the data owners.
The Portuguese Node has been testing and providing feedback for the Local EGA and Beacon v2 repositories. We
have successfully deployed a prototype of the LocalEGA with some of the components of these systems, namely
the connection to the Central EGA and the Ingestion system and the validation and upload components of
Beacon.
In spite of these milestones already achieved, we are facing difficulties with the implementation of the data
distribution system of the Local EGA and the API of the Beacon v2. We are working closely with the ELIXIR Spain
node and could benefit from short stays of the Portuguese team at CRG and from the Spanish team at INESC-ID
to overcome current hurdles in these implementations. In addition to enhancing the delivery by the ELIXIR PT, this
staff exchange will serve as a case-study to define such hurdles and troubleshooting measures that can be
extended to other nodes in the form of recommendations and tutorials, thus lowering the effort required for other
nodes to achieve their implementations.