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 https://progenetix.org/beacon/variants/
or https://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?filters=cellosaurus:CVCL_0004
- this example retrieves all biosamples having an annotation for the Cellosaurus CVCL_0004 identifier (K562)
/biosamples/{id}/
¶
- /biosamples/pgxbs-kftva5c9
- retrieval of a single biosample
/biosamples/?testMode=true
¶
- /biosamples?testMode=true
- retrieval of some random samples
- for testing API responses
/biosamples/{id}/g_variants
¶
- /biosamples/pgxbs-kftva5c9/g_variants/
- retrieval of all variants from a single biosample
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/pgxind-kftx25hb/
- retrieval of a single individual
/individuals/?testMode=true
¶
- /individuals?testMode=true
- retrieval of some random individuals
- for testing API responses
/individuals/{id}/g_variants
¶
- /individuals/pgxind-kftx25hb/g_variants/
- /individuals/pgxind-kftx25hb/genomicVariations/
- retrieval of all variants from a single individual
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?testMode=true
- retrieval of some random variants
- for testing API responses
/g_variants
+ query¶
- /variants/?assemblyId=GRCh38&referenceName=17&variantType=DEL&filterLogic=AND&start=7500000&start=7676592&end=7669607&end=7800000
- This is an example for a Beacon "Bracket Query" which will return focal deletions in the TP53 locus (by position).
/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/?testMode=true
- retrieval of some random analyses
- for testing API responses
/analyses
+ query¶
- /analyses?filters=cellosaurus:CVCL_0004
- this example retrieves all biosamples having an annotation for the Cellosaurus CVCL_0004 identifier (K562)
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 ofresult_sets
- 2021-06-24: Updated query structure conforming to v2b4
entityType
format fixedfilters
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