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endpoints.yaml
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endpoints.yaml
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openapi: 3.0.2
servers: []
info:
version: 2.0.0
title: GA4GH Beacon API Specification - Genomic Variations Endpoints
description: TBD
contact:
email: beacon@ga4gh.org
license:
name: Apache 2.0
url: https://www.apache.org/licenses/LICENSE-2.0.html
paths:
/g_variants:
get:
parameters:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- $ref: '#/components/parameters/includeResultsetResponses'
- $ref: '#/components/parameters/start'
- $ref: '#/components/parameters/end'
- $ref: '#/components/parameters/assemblyId'
- $ref: '#/components/parameters/referenceName'
- $ref: '#/components/parameters/referenceBases'
- $ref: '#/components/parameters/alternateBases'
- $ref: '#/components/parameters/variantMinLength'
- $ref: '#/components/parameters/variantMaxLength'
- $ref: '#/components/parameters/genomicAlleleShortForm'
- $ref: '#/components/parameters/geneId'
- $ref: '#/components/parameters/aminoacidChange'
- $ref: '#/components/parameters/filters'
description: Get a list of example entries
operationId: getExampleEntries
tags:
- GET Endpoints
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
description: Get a list of example entries
operationId: postExampleEntriesRequest
tags:
- POST Endpoints
requestBody:
content:
application/json:
schema:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json
required: true
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
/g_variants/{id}:
parameters:
- $ref: '#/components/parameters/entryId'
get:
description: Get details about one genomic variation, identified by its (unique)
'id'
operationId: getOneGenomicVariation
tags:
- GET Endpoints
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
description: Get details about one genomic variation, identified by its (unique)
'id'
operationId: postOneGenomicVariation
tags:
- POST Endpoints
requestBody:
content:
application/json:
schema:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json
required: true
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
/g_variants/{id}/biosamples:
parameters:
- $ref: '#/components/parameters/entryId'
get:
parameters:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
description: Get the biosamples list from one genomic variant, identified by
its (unique) 'id'
operationId: getOneGenomicVariantBiosamples
tags:
- GET Endpoints
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
description: Get the biosamples list from one genomic variant, identified by
its (unique) 'id'
operationId: postOneGenomicVariantBiosamples
tags:
- POST Endpoints
requestBody:
content:
application/json:
schema:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json
required: true
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
/g_variants/{id}/individuals:
parameters:
- $ref: '#/components/parameters/entryId'
get:
parameters:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
description: Get the individuals list from one genomic variant, identified by
its (unique) 'id'
operationId: getOneGenomicVariantIndividuals
tags:
- GET Endpoints
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
description: Get the biosamples list from one genomic variant, identified by
its (unique) 'id'
operationId: postOneGenomicVariantIndividuals
tags:
- POST Endpoints
requestBody:
content:
application/json:
schema:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json
required: true
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
default:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
components:
responses:
ResultsOKResponse:
description: Successful operation.
content:
application/json:
schema:
oneOf:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json
parameters:
requestedSchema:
name: requestedSchema
description: Schema to be used to format the `result` field in the response.
The response will use Beacon format.
in: query
required: false
schema:
type: string
example: ga4gh-service-info-v1.0
skip:
name: skip
in: query
schema:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
limit:
name: limit
in: query
schema:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
includeResultsetResponses:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses
entryId:
name: id
in: path
required: true
schema:
type: string
start:
name: start
in: query
schema:
type: array
items:
type: integer
format: int64
minimum: 0
minItems: 1
maxItems: 2
end:
name: end
in: query
schema:
type: array
items:
type: integer
format: int64
minimum: 0
minItems: 0
maxItems: 2
assemblyId:
name: assemblyId
in: query
schema:
type: string
referenceName:
name: referenceName
in: query
schema:
type: string
referenceBases:
name: referenceBases
in: query
schema:
type: string
alternateBases:
name: alternateBases
in: query
schema:
type: string
variantMinLength:
name: variantMinLength
in: query
schema:
type: integer
format: int64
minimum: 0
variantMaxLength:
name: variantMaxLength
in: query
schema:
type: integer
format: int64
minimum: 0
genomicAlleleShortForm:
name: allele
in: query
schema:
type: string
example: NM_004006.2:c.4375C>T
geneId:
name: geneid
in: query
schema:
type: string
example: BRAF
aminoacidChange:
name: aminoacidChange
in: query
schema:
type: string
example: V600E
filters:
name: filters
in: query
schema:
type: array
items:
type: string
examples:
- - EFO:0009655
- - NCIT:C48725
- NCIT:C28080