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 ...
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 ...
The topic of “EvidenceBeacon” was discussed with many different attendants during the speed datingg session and beyond, leading to some clearer picture about the (widening) extent & next steps.
@mbaudis 2019-04-30: 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 ...
Future Beacon API versions will support querying for additional, non-sequence related data types.
@mbaudis 2018-10-18: 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 2019-10-21: more ...
Beacon is an ever changing product, and it’s a good thing! Our partners in research and clinical settings are helping us improve version 2, who will soon be submitted for approval to GA4GH. Here is a list of resources, with their corresponding versions, to help you navigate our documentation while we prepare a beautiful repository just for you.
Version 2, draft 3:
Version 2, draft 2:
The reference implementation is in progress: a version compliant with draft 1.5 can be found here.
@laurenfromont 2021-03-02: more ...
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 ...
These are the official repositories for version 2 of the specification and the Reference Implementation:
@mbaudis | @sdelatorrep 2021-02-22: more ...