GA4GH Beacon API Specification - Cohorts Endpoints (2.0.0)

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

TBD

GET Endpoints

Available endpoints in this API. All of them have a POST counterpart.

getCohorts

Get a list of cohorts

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=OMIABIS:0001017

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
}
}

getOneCohort

Get details about one cohort, 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.

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
}
}

getOneCohortIndividuals

Get the individuals from one cohort, 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
}
}

getOneCohortFilteringTerms

Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'

path Parameters

required

string

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

The same operations than GET, just by POST.

postCohortsRequest

Get a list of cohorts

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
}
}

postOneCohort

Get details about one cohort, 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
}
}

postOneCohortEntries

Get the individuals from one cohort, 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
}
}

postOneCohortFilteringTerms

Get the list of filtering terms that could be used with a given cohort, 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

{"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"
}
]
}
}