Beacon v2 Workshop at ELIXIR All Hands

Beacon implementations: Beaconize your genomics data

Hosts: Lauren Fromont & Jordi Rambla

One of the main bottlenecks in human genomics research is the lack of tools for federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention since genomics data sees an ever greater application in clinical settings, such as for medical diagnostic or prognostic purposes, in rare diseases or cancer. Currently, most of the molecular analyses generated in hospitals are not utilised for further research due to lack of proper tools for an interoperable and ethical sharing of the data. The Beacon project (ELIXIR, see also the Global Alliance in Health and Genomics for the standard) aims to alleviate the problem of genomics data sharing through enabling the search of genomic variants and associated information without jeopardising the privacy of the dataset. This way, any hospital or research entity can choose to ‘beaconize’ their dataset without compromising its privacy or ownership.

With growing interest from the community in the implementation of the Beacon protocol into resources and workflows, the release 2.0 introduces new features considered important by the community: e.g. queries by entity type, filters, schema versions, and access levels. While both the research and the clinical community recognizes the value of these additions, practical implementation of the Beacon could still be a challenging task, especially for institutions with limited IT resources. The ELIXIR implementation studies (2019-2021; 2022-2024) aim to develop a reference implementation so researchers and clinicians can use it as an example to deploy their own Beacon without needing extensive knowledge on how to build an API.

This workshop has two objectives, to provide participants with:

1- Demos and insights on Beacon implementations. For this objective we will invite early Beacon v2 implementers who provided valuable feedback to the specification and will share their use-cases and experiences: Michael Baudis (Progenetix), Tim Beck (Café Variome), and Carles Hernandez (CNAG-CRG).

2- A training session on how to d eploy a Beacon using the reference implementation. For this objective we will invite members of the European Genome-phenome Archive (Manuel Rueda) who support Beacon deployment in hospitals and clinical institutions and will provide a hands-on session.

Beacon version 2 is a highly expected product in the genomics research and clinical communities. Now that the Beacon community has released a stable version, it is time to provide beacon implementers guidelines and resources to implement or deploy their own Beacons to foster data discovery and data re-use.

@laurenfromont 2022-04-06
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