Genomic “Beacons” provide discovery services for genomic data using the Beacon API developed as a key driver project of the Global Alliance for Genomics and Health (GA4GH). The Beacon protocol itself defines an open standard for genomics data discovery and provides a framework for web services responding to queries against genomic data collections, for instance from population based or disease specific genome repositories. Sites offering beacons can scale through aggregation in “Beacon Networks” which distribute queries among a potentially large number of beacons and assemble their responses.
As part of ELIXIR’s Beacon 2019–21 project work has advanced on a re-designed Beacon protocol, with the aim to provide a maximum of flexibility while closely adhering to data and security standards promoted by the international research community, aligned with the GA4GH ecosystem. Beacon v2 features have been designed with view to clinical and biomedical research, e.g. for variant evidence and annotation data or the retrieval of diagnostic and other clinical data when used in secure environments. Recently, the efficient use of the Beacon protocol for non-human genome data has been demonstrated for COVID-19 repositories, showcasing the flexibility of the protocol.
Here I will provide an overview about the history, current status future directions of the Beacon protocol, including details about the Beacon+ service on top of the progenetix.org cancer genomics resource.