Implementation

How to implement a Beacon

Framework & Model

Types of beacon

You should decide which type of beacon you want:

Granularity	Description
boolean	Only returns exists: true ('Yes') or exists: false ('No') to a given query.
count	Returns exists: true or exists: false and the total number of positive results found (numTotalResults).
record	Returns all of the previous information and adds details for every row.

We recommend starting with a boolean beacon and the upgrading its capabilities.

Endpoints

Configuration endpoints

/info and also the root (/)

It MUST return information (metadata) about the Beacon service and the organization supporting it.

Response schema: beaconInfoResponse.json

Example:

/service-info

It returns the Beacon metadata in the GA4GH Service Info schema.

Response schema: ga4gh-service-info-1-0-0-schema.json

Example:

/configuration

It returns some configuration aspects and the definition of the entry types (e.g. genomic variants, biosamples, cohorts) implemented in that specific Beacon server or instance.

Response schema: beaconConfigurationSchema.json

Example:

/entry_types

It returns only the property entryTypes of the /configuration endpoint.

Response schema: beaconConfigurationSchema.json -> EntryTypes

Example:

/map

It returns a map (like a web sitemap) of the different endpoints implemented in that Beacon instance.

Response schema: beaconMapSchema.json

Example:

/filtering_terms

It returns a list of the filtering terms accepted by that Beacon instance.

Response schema: filteringTermsSchema.json

Example:

For more examples, visit: https://github.com/ga4gh-beacon/beacon-framework-v2

Entities

Entity	Default Schemas	Endpoints
Analyses	defaultSchema.json	analyses analyses/{id} analyses/{id}/g_variants
Biosamples	defaultSchema.json	biosamples biosamples/{id} biosamples/{id}/g_variants biosamples/{id}/analyses biosamples/{id}/runs
Cohorts	defaultSchema.json	cohorts cohorts/{id} cohorts/{id}/individuals cohorts/{id}/filtering_terms cohorts/{id}/runs cohorts/{id}/analyses
Datasets	defaultSchema.json	datasets datasets/{id} datasets/{id}/g_variants datasets/{id}/biosamples datasets/{id}/individuals datasets/{id}/filtering_terms datasets/{id}/runs datasets/{id}/analyses
Genomic Variations	defaultSchema.json	g_variants g_variants/{id} g_variants/{id}/biosamples g_variants/{id}/individuals g_variants/{id}/runs g_variants/{id}/analyses
Individuals	defaultSchema.json	individuals individuals/{id} individuals/{id}/g_variants individuals/{id}/biosamples individuals/{id}/filtering_terms individuals/{id}/runs individuals/{id}/analysis
Runs	defaultSchema.json	runs runs/{id} runs/{id}/g_variants runs/{id}/analyses