GA4GH Beacon API Specification - Individuals Endpoints (2.0.0)

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

TBD

GET Endpoints

getIndividuals

Get a list of individuals

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:C20197

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
}
}

getOneIndividual

Get details about one individual, 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
}
}

getOneIndividualGenomicVariants

Get the genomic variants list from one individual, 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
}
}

getOneIndividualBiosamples

Get the biosamples list from one individual, 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
}
}

getIndivualsFilteringTerms

Get the list of filtering terms that could be used with individuals.

query Parameters

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

{"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"response": {"filteringTerms": [{"id": "HP:0008773",
"label": "Aplasia/Hypoplasia of the middle ear",
"type": "Human Phenotype Ontology"
}
],
"resources": [{"id": "hp",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_",
"name": "Human Phenotype Ontology",
"nameSpacePrefix": "HP",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "17-06-2019"
}
]
}
}

POST Endpoints

postIndividualsRequest

Get a list of example entries

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
}
}

postOneIndividual

Get details about one Individual, 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
}
}

potOneIndividualGenomicVariants

Get the genomic variants list from one individual, 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
}
}

postOneIndividualBiosamples

Get the biosamples list from one individual, 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
}
}

postIndividualsFilteringTerms

Get the list of filtering terms that could be used with individuals.

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

{"meta": {"apiVersion": "v2.0",
"beaconId": "org.example.beacon.v2",
"returnedSchemas": [{"entityType": "Individual",
"schema": "./ga4gh-beacon-dataset-v2.0.0"
}
]
},
"response": {"filteringTerms": [{"id": "HP:0008773",
"label": "Aplasia/Hypoplasia of the middle ear",
"type": "Human Phenotype Ontology"
}
],
"resources": [{"id": "hp",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_",
"name": "Human Phenotype Ontology",
"nameSpacePrefix": "HP",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "17-06-2019"
}
]
}
}