REST API for Oracle Healthcare Translational Research

Retrieve Variants for Prediction and Chromosome

get

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

This endpoint supports the retrieval of Variant Identifiers for Chromosome, Start Position, End Position, Assembly/Alignment Identifier, Prediction Type, multiple Prediction Code, Prediction Score and Prediction Comparator. The response fetches Variants Identifiers which are having defined prediction code or score. Both SIFT and PolyPhen (Polymorphism Phenotyping) type data can be searched using this API.

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

predictionCode

Type: array

Collection Format: multi

List of Prediction Codes. For ex.,deleterious

Items

Type: string

predictionComparator

Type: string

Prediction Score Comparator( < , > , = )

predictionScore

Type: string

Prediction Score .For ex.,1

predictionType

Type: string

Required: true

Prediction Type. for ex.,SIFT

startPosition

Type: integer (int64)

Required: true

Start location of sequence

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

Chromosome End Position is not supplied

404 Response

Variants not found for the Chromosome and Prediction details supplied

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/variants/byPrediction/byChromosome?chromosome=CHR&startPosition=10250&endPosition=10251&predictionType=SIFT&predictionScore=1&predictionComparator=<&alignmentId=1&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
   "resourceType":"Variants",
   "items":[
      {
         "identifier":{
            "system":"ODB",
            "value":"536778"
         },
         "variantPrediction":{
            "reference":"/HSDataService-web/api/3.2.0/variants/536778/variantPredictions"
         }
      },
      {
         "identifier":{
            "system":"ODB",
            "value":"536777"
         },
         "variantPrediction":{
            "reference":"/HSDataService-web/api/3.2.0/variants/536777/variantPredictions"
         }
      }
   ],
   "count":2,
   "hasMore":false,
   "links":[
      {
         "rel":"self",
         "href":"http://localhost:7001/HSDataService-web/api/3.2.0/variants/byPrediction/byChromosome?chromosome=CHR&startPosition=10250&endPosition=10251&predictionType=SIFT&predictionScore=1&predictionComparator=<&alignmentId=1&limit=10&offset=0"
      }
   ]
}