Welcome to the Beacon v2 Documentation¶
A Standard of the Global Alliance for Genomics and Health GA4GH
On 2022-04-21 Beacon v2 has been approved as an official GA4GH standard through the GA4GH steering committee.
With growing interest from the community in the implementation of the Beacon protocol into resources and workflows, the major 2.0 release in 2022 introduced a large range of new features which were considered important by the community.
Move to Beacon v2
With the release of Beacon v2 implementations of v1 and earlier are not longer supported. Deployers of Beacon instances or networks are advised to migrate to v2 of the standard. The functionality of Beacon v1 can be easily implemented in v2.
The core documentation (i.e. this document) can be found on here. Additional information about the Beacon project - including news, events, publications - is available through the website beacon-project.io.
Informations for Different Types of Beacon Users¶
The Beacon documentation provides information for different types of users, depending on their interests and use cases. Although those will overlap, we highlight information relevant for some general scenarios throughout the documentation.
A Beacon user (or end-user) is interested in querying Beacon instances and networks, either through web interfaces by using the Beacon API. While users of Beacon web forms in principle do not need to understand the underlying query syntax and response formats they too may benefit from some insights into the general capabilities of the underlying protocol.
- Beacon v2 Models
- Knowing what is available in an instance
- Data Models and Schemas
- Beacon Flavours & Response Granularity
- Other Request, Response & Error Elements
- Using Beacon v2 Features
- Genomic Variant Queries
- Filters for Phenotypes, Diseases & Other Parameters
- Alternative Schemas Link
Deployers and Implementers¶
A Beacon Deployer is someone who wants to make their genomics resource accessible through the Beacon protocol, without necessarily being interested or experienced in the computational aspects; while a Beacon Implementer provides the technical expertise (and potentially may get involved with Beacon development itself, e.g. to extend the protocol for novel use cases).
Beacon v2 Models
Reference Implementation Link
- Infrastructure requirements
- How to install
- Cohorts and/or Datasets
- Entry types
- Filtering terms
- Alternative schemas
- Granularity & Security
- Testing the instance
- Integration into GA4GH
- Leveraging The Beacon Framework in other domains
- Success Stories:
- Real world data