Any publica data resource containing “human derived” data has a potential for re-identification attacks, that is the identification of individuals contributing data to the resource.
Since its inception, the Beacon Project has been actively working with experts in GA4GH’s membership to address potential privacy concerns.
@mbaudis 2018-10-17: more ...
A Beacon is an online web service that allows users to query an institution’s databases, to determine whether they contain a genetic variant of interest. The query is structured as a yes/no question of the form: “Do you have any genomes with an ‘X’ at position Y on chromosome Z?”
@mbaudis 2018-10-17: 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 ...
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 ...
When an institution “lights” a Beacon, it demonstrates its willingness and ability to share data.
@mbaudis 2018-10-18: more ...
In current medical practice, doctors commonly share basic, de-identified information about patients’ conditions and genetic variations in the hopes of matching a second case that could be therapeutically transformative. This practice is a long-standing tradition in the medical community but it is neither standardized nor optimized. The Beacon Project turns that informal transaction into a more efficient and effective search that can be a key initial step for learning from valuable genomic information.
@mbaudis 2018-10-18: more ...
Beacons present an easy-to-implement strategy for determining whether an institution has genomic data in its data set that would be useful to share.
@mbaudis 2018-10-18: more ...
In an ideal scenario, your Github served website could be build locally, with the same output structure and layout.
@mbaudis 2019-03-14: more ...
The coordinate system that should be used throughout GA4GH standards is 0-based half open.
@mbaudis 2019-03-14: more ...
The Progenetix Jekyll template modifies the standard Jekyll file structure.
@mbaudis 2019-03-14: more ...
The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.
@mbaudis 2019-03-14: more ...
New pages are added to the website inside one of the “collections” directories in the /
directory. This can either be done by adding files locally or on Github (if hosted there).
@mbaudis 2019-03-25: more ...
An open-access online tutorial How to install and deploy Beacon has been launched on the ELIXIR-SI eLearning Platform (EeLP). Learning materials are provided by ELIXIR Beacon project contributors from Finland and Spain.
The tutorial is registered on ELIXIR Training eSupport System (TeSS) and contains instructions for Beacon installation and deployment, both as instruction manual and tutorial video. No username and password is required to access the tutorial.
@markowhatever 2019-03-26: more ...