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 ...
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 ...
Beacon v0.4.0 has been released using the OpenAPI specification.
@mbaudis 2018-01-24: more ...
Beacon v0.3.0 Release
@mbaudis 2016-05-31: more ...
This page provides some more detailed description of the “4 positions match any continuous region” concept. General examples for variant queries can be found in the “Example Queries” documentation.
@mbaudis 2018-10-17: more ...
The coordinate system that should be used throughout GA4GH standards is 0-based half open.
@mbaudis 2019-03-14: more ...
The official Beacon API v1.0.0 has been approved through the GA4GH Product Approval Process.
@mbaudis 2018-10-02: more ...
Precise variants are such with annotated sequences of 0….n length, and bases
of [ATCGN] for the referenceBases and alternateBases attributes (N for
“not specified”).
Examples for variant queries can be found in the “Example Queries” documentation.
@mbaudis 2018-10-17: 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 ...
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 ...
Today the Github repositories for the Beacon v2 specification have been created:
@mbaudis | @sdelatorrep 2020-01-14: more ...