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Org.progenetix

Progenetix & Beacon+

The Beacon+ implementation - developed in the Python & MongoDB based bycon project - implements an expanding set of Beacon v2 paths for the Progenetix resource 🇨🇭.

Scoped responses from query object

In queries with a complete beaconRequestBody the type of the delivered data is independent of the path and determined in the requestedSchemas. So far, Beacon+ will compare the first of those to its supported responses and provide the results accordingly; it doesn't matter if the endpoint was /beacon/biosamples/ or /beacon/variants/ etc.

Below is an example for the standard test "small deletion CNVs in the CDKN2A locus, in gliomas" Progenetix test query, here responding with the matched variants. Exchanging the entityType entry to

  • { "entityType": "biosample", "schema:": "https://progenetix.org/services/schemas/Biosample/"}

would change this to a biosample response. The example ccan be tested by POSTing this as application/json to http://progenetix.org/beacon/variants/ or http://progenetix.org/beacon/biosamples/.

{
    "$schema":"beaconRequestBody.json",
    "meta": {
        "apiVersion": "2.0",
        "requestedSchemas": [
            {
                "entityType": "genomicVariant",
                "schema:": "https://progenetix.org/services/schemas/genomicVariant"
            }
        ]
    },
    "query": {
        "requestParameters": {
            "datasets": {
                "datasetIds": ["progenetix"]
            },
            "assemblyid": "GRCh38",
            "referenceName": "9",
            "start": [21500001, 21975098],
            "end": [21967753, 22500000], 
            "variantType": "DEL"
        }
    },
    "filters": [
        { "id": "NCIT:C3058", "includeDescendantTerms": true }
    ]
}

Paths

Base /

The root path provides the standard BeaconInfoResponse.


Base /filtering_terms

/filtering_terms/

Base /biosamples

/biosamples/ + query
/biosamples/{id}/
/biosamples/?testMode=true
/biosamples/{id}/g_variants

Base /individuals

/individuals + query
  • /individuals?filters=NCIT:C7541
  • this example retrieves all individuals having an annotation associated with NCIT:C7541 (retinoblastoma)
  • in Progenetix, this particular code will be part of the annotation for the biosample(s) associated with the returned individual
  • /individuals/?filters=PATO:0020001,NCIT:C9291
  • this query returns information about individuals with an anal carcinoma (NCIT:C9291) and a known male genotypic sex (PATO:0020001)
  • in Progenetix, the information about its sex is associated with the Individual object (and therefore in the individuals collection), whereas the information about the cancer type is a property of the Biosample (and therefore stored in the biosamples collection)
/individuals + query + requestedSchema=phenopacket

Progenetix provides phenopacket as (currently experimental) alternative schema (requestedSchema) for /individuals. This feature allows the combined delivery of attributes annotated w/ the biosamples and such general of the individual, as well as e.g. linking to genomic variation data.

/individuals/{id}
/individuals/?testMode=true
/individuals/{id}/g_variants

Base /g_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.

variants is used as alias.

/g_variants?testMode=true
/g_variants + query
/g_variants/{id}
/g_variants/{id}/biosamples

Base /analyses

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.

/callsets is an alias in Progenetix

/analyses?testMode=true
/analyses + query

Changes

  • 2022-04-17: removed some non-standard examples (e.g. variants_in_sample)
  • 2021-11-02: added /testMode example
  • 2021-07-21: added /map endpoint (incomplete/unser construction)
  • 2021-07-21: added /configuration endpoint (incomplete/unser construction)
  • 2021-07-02: update for /filteringTerms endpoint to v2b4
  • 2021-06-25: updated for datasets parameter as object
  • 2021-06-24: Updated response structure conforming to v2b4:
  • response_summary
  • removal of response root element & direct use of result_sets
  • 2021-06-24: Updated query structure conforming to v2b4
  • entityType format fixed
  • filters now objects
  • 2021-06-23: New JSON POST example & topic
  • 2021-06-07: Added variants_interpretations example
  • 2021-05-29: New resultSets response format
  • no change to front-end or examples here but change of bycon backend
  • 2021-05-11: Added /analyses
  • 2021-05-02: Added base path for BeaconInfoResponse
  • 2021-04-26: First Version