REST API for Oracle Healthcare Translational Research

Retrieve Variants for Variant Effect and Chromosome

get

/HSDataService-web/api/3.2.0/variants/byEffect/byChromosome

This endpoint supports the retrieval of Variant Identifiers for Variant Effect, Chromosome, Start Position, End Position and Assembly/Alignment Identifier.

Request

Supported Media Types

application/json
application/xml

Query Parameters

alignmentId: Type: integer (int64)

Required: true

Assembly/Alignment ID
chromosome: Type: string

Required: true

Chromosome Name. For ex.,'Y'
endPosition: Type: integer (int64)

Required: true

Chromosome End Position
limit: Type: integer (int32)

Number of rows to return
offset: Type: integer (int32)

Row number to start from
startPosition: Type: integer (int64)

Required: true

Start location of sequence
variantEffect: Type: string

Required: true

Variant Effect

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Model for paginated collections of data.

Root Schema : PageableCollectionVariant

Type: object

Model for paginated collections of data.

Properties

count: Type: integer (int64)

Number of objects in the 'items' collection.
hasMore: Type: boolean

Default Value: false

A boolean indicating if more pages are available.
items: Type: array items

A collection of paged items.
links: Type: array links

A collection of links containing hrefs to the current, next, and previous pages as applicable.
resourceType: Type: string

Identify the resource type

Nested Schema : items

Type: array

A collection of paged items.

Items

Type: object Variant

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

Example

{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}

Items

Type: string

Nested Schema : Variant

Type: object

Properties

identifier: Type: object Identifier

Identifier assigned by a given system
variantPrediction: Type: object LinkedReference

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

Properties

system: Type: string

System which assigned this identifier
value: Type: string

Identifier value

Nested Schema : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

400 Response

Filter Variants input is not valid

404 Response

Variants not found for the Chromosome and VariantEffect supplied

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/variants/byEffect/byChromosome?alignmentId=1&chromosome=CHR&startPosition=10250&endPosition=10251&variantEffect=synonymous&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "items":[
  {
  "identifier":"138260072"
  }
  ]
  "count": 1,
  "hasMore": false,
  "links" : [ {
     "rel" : "self",
     "href" : "http://localhost:7001/HSDataService-web/api/3.2.0/variants/byEffect/byChromosome?alignmentId=1&chromosome=CHR&startPosition=10250&endPosition=10251&variantEffect=synonymous&limit=10&offset=0"
   } ] 
}