Biosamples: samples taken from individuals, including details of procedures, dates and times.

Individuals: either patients or healthy controls whose details (including phenotypic and clinical) are stored in the repository.

Genomic variations: unique genomic alterations, e.g., position in a genome, sequence alterations, type, etc.

Collections: groupings of variants or individuals that share something in common: e.g., who belong to the same repository ( datasets) or study population ( cohorts).

The following entities are defined as follows (the links lead to the field descriptions): Schematic representation of the Beacon v2 logical Model Check out the Documentation for Beacon v2 Model’s default schema. It covers the different entities and details arising from clinical requirements.

Examples for all the abovementioned elements (using a mock and simple Model).

The JSON schemas for the requests, the responses, and its respective sections.

The Framework repo includes the elements that are common to all Beacons: Handling the Framework to deploy your own Beacon requires experience with APIs. It is the structure upon which the whole API is built. If Beacon v2 were a language, the Framework would be the Syntax. However, in the current context of Beacon v2, we consider the two elements interdependent and likely to be updated together for subsequent major versions (e.g. “Imaging Beacon”) to be built using the same Framework. In principle, this concept allows for different Models (in other domains outside of the Beacon v2 realm, e.g. The Model has been developed for biomedical stakeholders.

The Beacon Model describe the set of concepts included in Beacon V2, like individual or biosample, and also the relationships between them.

The Beacon Framework is the part that describes the overall structure of the API requests, responses, parameters, the common components, etc.

The Beacon v2 is based on a two-part concept, with the following documents covering essential aspects of the specification: Schematic example of a Beacon query (version 2) Beacon v2 scope

Annotations about the variants found, among which the expert/clinician conclusion about the pathogenicity of a given mutation in a given individual or its role in producing a given phenotype įigure 3.

if the Beacon is for internal use of the hospital, to provide the Id of the EHR of the patients having the mutation of interest

An option to jump to another system where the data could be accessed, e.g.

who to contact or which are the data use conditions

An option to trigger the next step in the data access process, e.g.

Query options for biological or technical “meta”data using fiters defined through CURIEs (e.g.

The version 2 (v2) of the Beacon protocol has been accepted as GA4GH standard in Spring 2022. Schematic example of a Beacon query (up to version 1)

Examples can be found in the ELIXIR Beacon network page. Originally, the Beacon protocol (versions 0 and 1) allowed researchers to get information about the presence/absence of a given, specific, genomic mutation in a set of data, from patients of a given disease or from the population in general (Figure 2).

What is Beacon?īeacon is an API (sometimes extended with a user interface) that allows for data discovery of genomic and phenoclinic data. This way, any hospital or research entity can choose to ‘beaconize’ their omics dataset without compromising the privacy or the ownership of the dataset, thus helping the worldwide community of researchers and assisting science through the power of data. The Beacon API aims to solve this problem through enabling the search of genomic variants and associated information without jeopardising the privacy of the dataset. In the time of personalised medicines, inclusive diagnostics, prognostic and therapeutic strategies, we simply cannot afford to keep the data locked in. This further slows down the progress in research. Genomics data is identifiable and therefore needs to be protected, however, due to lack of data security infrastructure and good health data practices, it forces clinicians and researchers to not share their data at all. One of the main bottlenecks in human genomics research is lack of data.

The Beacon Project is developed under an initiative by Global Alliance for Genomics and Health (GA4GH) for the federated discovery of genomic data in biomedical research and clinical applications. (A) Beacon API implementation and (B) A Beacon query and aggregated responseĪ Beacon is a simple genomics variant discovery tool by aggregating worldwide genomics dataset under one umbrella. A schematic representation of how Beacon works. How do I test a Beacon without having to go through complex security matters (yet)?.How is security actually implemented when I deploy a Beacon?.What are the general security principles for Beacon?.I want to deploy a Beacon: how does this affect me?.

Beacon designer download