Beacon v2: Path Examples

The Beacon v2 protocol uses a REST path structure for consistant data access.

The Beacon+ implementation - developed oin the bycon project implements an expanding set of those Beacon v2 paths for the Progenetix resource.

Base /

The root path provides the standard BeaconInfoResponse.

Base /filtering_terms

/filtering_terms/ + query

Base /biosamples

/biosamples/ + query
/biosamples/{id}/variants/ & /biosamples/{id}/variants_in_sample/

Base /individuals

/individuals/ + query
/individuals/{id}/variants/ & /individuals/{id}/variants_in_sample/

Base /variants

There is currently (April 2021) still some discussion about the implementation and naming of the different types of genomic variant endpoints. Since the Progenetix collections follow a “variant observations” principle all variant requests are directed against the local variants collection.

If using g_variants or variants_in_sample, those will be treated as aliases.

/variants/ + query
/variants/{id}/ or /variants_in_sample/{id} or /g_variants/{id}/
/variants/{id}/biosamples/ & variants_in_sample/{id}/biosamples/

Base /analyses (or /callsets)

The Beacon v2 /analyses endpoint accesses the Progenetix callsets collection documents, i.e. information about the genomic variants derived from a single analysis. In Progenetix the main use of these documents is the storage of e.g. CNV statistics or binned genome calls.

/analyses/ + query


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