An v2 extension of the Beacon protocol will allow the query for additional
data beyond genome variants, using a proposed
filters extension. Such filters
are thought to be prefixed attributes, where the (public or private) prefix
becomes the basis of scoping the value to the correct database value.
@tb143 | @mbaudis 2020-05-12: more ...
In the original Beacon roadmap definitions, “clinical Beacon” (lower case) described a set of use cases instead of a specific Beacon flavour.
2020-03-23: more ...
The Beacon Project is a Global Alliance for Genomics and Health (GA4GH) initiative for the federated discovery of genomic data in biomedical research and clinical applications. Originally implemented as a tool reporting the existence of Single Nucleotide Polymorphisms (SNP) in aggregated genomic data collections, the protocol has evolved towards more complex applications with increased functionality. Implementations of the current Beacon API enable the search for structural variants (e.g. deletions and duplications) and return richer responses (e.g. variant metadata and call counts).
@mbaudis | @laurenfromont 2019-10-21: more ...
Instead of querying for a specific genomic variant (e.g. an
A instead of a
G at position
7577121 on chromosome
17), Beacons could also employ a “range match” concept, in which all or type specific variants mapping to a genomic interval are being identified.
@mbaudis 2018-11-16: more ...
Beacons may be able to increase their functionality through the development of distinct flavours, which can extend the core Beacon concept for specific use cases.
@mbaudis 2018-10-24: more ...
While the Beacon response should be restricted to aggregate data (yes/no, counts, frequencies …), the usage of the protocol could be greatly expanded by providing an access method to data elements matched by a Beacon query.
As part of the mid-term product strategy, the ELIXIR Beacon team is evaluating the use of a “handover” protocol, in which rich data content (e.g. variant data, phenotypic information, low-level sequencing results) can be provided from linked services, initiated through a Beacon query (and possibly additional steps like protocol selection, authentication…). A discussion of the topic can e.g. be found in the Beacon developer area on Github (issue #114).
As of 2018-11-13, the handover concept has become part of the ongoing code development.
@mbaudis 2018-10-18: more ...