GA4GH Beacon API Specification - Biosamples endpoints (2.0.0)

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E-mail: beacon@ga4gh.org License: Apache 2.0

TBD

GET Endpoints

getBiosamples

Get a list of biosamples

query Parameters

requestedSchema	string Example: requestedSchema=ga4gh-service-info-v1.0 Schema to be used to format the `result` field in the response. The response will use Beacon format.
skip	integer (Skip) >= 0 Default: 0 Example: skip=0 In the request: number of pages to skip * In the response: number of pages that has been skipped
limit	integer (Limit) >= 0 Default: 10 Example: limit=10 Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.
filters	Array of strings Examples: filters=NCIT:C3222 filters=OBI:0100058&filters=NCIT:C4813

Responses

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

getOneBiosample

Get details about one biosample, identified by its (unique) 'id'

path Parameters

required

string

Responses

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

getOneBiosampleGenomicVariants

Get the genomic variants list from one biosample, identified by its (unique) 'id'

path Parameters

required

string

query Parameters

requestedSchema	string Example: requestedSchema=ga4gh-service-info-v1.0 Schema to be used to format the `result` field in the response. The response will use Beacon format.
skip	integer (Skip) >= 0 Default: 0 Example: skip=0 In the request: number of pages to skip * In the response: number of pages that has been skipped
limit	integer (Limit) >= 0 Default: 10 Example: limit=10 Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.

Responses

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

getOneBiosampleAnalysis

Get the analysis list from one biosample, identified by its (unique) 'id'

path Parameters

required

string

query Parameters

requestedSchema	string Example: requestedSchema=ga4gh-service-info-v1.0 Schema to be used to format the `result` field in the response. The response will use Beacon format.
skip	integer (Skip) >= 0 Default: 0 Example: skip=0 In the request: number of pages to skip * In the response: number of pages that has been skipped
limit	integer (Limit) >= 0 Default: 10 Example: limit=10 Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.

Responses

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

getOneBiosampleRuns

Get the runs list from one biosample, identified by its (unique) 'id'

path Parameters

required

string

query Parameters

requestedSchema	string Example: requestedSchema=ga4gh-service-info-v1.0 Schema to be used to format the `result` field in the response. The response will use Beacon format.
skip	integer (Skip) >= 0 Default: 0 Example: skip=0 In the request: number of pages to skip * In the response: number of pages that has been skipped
limit	integer (Limit) >= 0 Default: 10 Example: limit=10 Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.

Responses

Response samples

Content type

application/json

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"response": {"$schema": "string",
"resultSets": [{"exists": true,
"id": "datasetA",
"info": { },
"results": [{ }
],
"resultsCount": 0,
"resultsHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"setType": "dataset"
}
]
},
"responseSummary": {"exists": true,
"numTotalResults": 123
}
}

POST Endpoints

postBiosamplesRequest

Get a list of biosamples

Request Body schema: application/json

$schema	string ($schema) Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.
required	object (beaconRequestMeta) Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.
	object Parameters to limit the list of returned results.

Responses

Request samples

Payload

Content type

application/json

{"$schema": "string",
"meta": {"$schema": "string",
"apiVersion": "v2.0",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"query": {"filters": [{"id": "HP:0002664",
"includeDescendantTerms": true,
"scope": "biosamples",
"similarity": "exact"
}
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"testMode": false
}
}

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

postOneBiosample

Get details about one Biosample, identified by its (unique) 'id'

path Parameters

required

string

Request Body schema: application/json

$schema	string ($schema) Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.
required	object (beaconRequestMeta) Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.
	object Parameters to limit the list of returned results.

Responses

Request samples

Payload

Content type

application/json

{"$schema": "string",
"meta": {"$schema": "string",
"apiVersion": "v2.0",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"query": {"filters": [{"id": "HP:0002664",
"includeDescendantTerms": true,
"scope": "biosamples",
"similarity": "exact"
}
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"testMode": false
}
}

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

postOneBiosampleGenomicVariants

Get the genomic variants list from one biosample, identified by its (unique) 'id'

path Parameters

required

string

Request Body schema: application/json

$schema	string ($schema) Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.
required	object (beaconRequestMeta) Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.
	object Parameters to limit the list of returned results.

Responses

Request samples

Payload

Content type

application/json

{"$schema": "string",
"meta": {"$schema": "string",
"apiVersion": "v2.0",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"query": {"filters": [{"id": "HP:0002664",
"includeDescendantTerms": true,
"scope": "biosamples",
"similarity": "exact"
}
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"testMode": false
}
}

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

postOneBiosampleAnalysis

Get the analysis list from one biosample, identified by its (unique) 'id'

path Parameters

required

string

Request Body schema: application/json

$schema	string ($schema) Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.
required	object (beaconRequestMeta) Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.
	object Parameters to limit the list of returned results.

Responses

Request samples

Payload

Content type

application/json

{"$schema": "string",
"meta": {"$schema": "string",
"apiVersion": "v2.0",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"query": {"filters": [{"id": "HP:0002664",
"includeDescendantTerms": true,
"scope": "biosamples",
"similarity": "exact"
}
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"testMode": false
}
}

Response samples

Content type

application/json

Example

beaconBooleanResponse

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"responseSummary": {"exists": true
}
}

postOneBiosampleRuns

Get the runs list from one biosample, identified by its (unique) 'id'

path Parameters

required

string

Request Body schema: application/json

$schema	string ($schema) Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.
required	object (beaconRequestMeta) Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.
	object Parameters to limit the list of returned results.

Responses

Request samples

Payload

Content type

application/json

{"$schema": "string",
"meta": {"$schema": "string",
"apiVersion": "v2.0",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"query": {"filters": [{"id": "HP:0002664",
"includeDescendantTerms": true,
"scope": "biosamples",
"similarity": "exact"
}
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"testMode": false
}
}

Response samples

Content type

application/json

{"beaconHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"info": { },
"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"receivedRequestSummary": {"apiVersion": "v2.0",
"filters": ["BTO:0000199",
"PATO:0000383"
],
"includeResultsetResponses": "ALL",
"pagination": {"currentPage": "ab0sc&fe1dd",
"limit": 10,
"nextPage": "ab0sc&fe1dd",
"previousPage": "ab0sc&fe1dd",
"skip": 0
},
"requestParameters": {"$schema": "string",
"property1": { },
"property2": { }
},
"requestedGranularity": "boolean",
"requestedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"returnedGranularity": "boolean",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
],
"testMode": false
},
"response": {"$schema": "string",
"resultSets": [{"exists": true,
"id": "datasetA",
"info": { },
"results": [{ }
],
"resultsCount": 0,
"resultsHandovers": [{"handoverType": {"id": "ga4gh:GA.01234abcde",
"label": "string"
},
"note": "This handover link provides access to a summarized VCF.",
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/"
}
],
"setType": "dataset"
}
]
},
"responseSummary": {"exists": true,
"numTotalResults": 123
}
}