REST API for Oracle Healthcare Translational Research

Retrieve Genomic Positions for a Gene Identifier

get

/HSDataService-web/api/3.2.0/genes/{id}/genomicPositions

This endpoint supports the retrieval of Genomic Positions for a single Gene Row ID passed. It returns Genomic Position information like Genomic Position, HUGO Name, Ensembl Name and other Genomic Position associated information.

Request

Supported Media Types

application/json
application/xml

Path Parameters

id: Type: integer (int64)

Required: true

gene row ID

Query Parameters

limit: Type: integer (int32)

Pagination query params: ?limit=2&offset=0
offset: Type: integer (int32)

Pagination query params: ?limit=2&offset=0

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Model for paginated collections of data.

Root Schema : PageableCollectionGenePosition

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 GenePosition

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 : GenePosition

Type: object

Properties

assembly: Type: string

Assembly/Alignment Name. For ex.,GRCh38
geneReference: Type: object LinkedReference
genomicPosition: Type: object GenomicPosition
hugoName: Type: string

Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc.
identifier: Type: object OdbIdentifier

Identifier assigned by a given system

Nested Schema : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

Nested Schema : GenomicPosition

Type: object

Properties

chromosome: Type: string

Chromosome Name. For ex.,'Y'
chromosomeId: Type: string
chromosomeName: Type: string

Chromosome Name. For ex.,'Y'
dateOfLoading: Type: string (date-time)

Insert Date
dnaReferenceVersion: Type: string

Version Label. For ex.,SIFT_VER2_75
endPosition: Type: integer (int64)

End location of sequence
ensemblReleaseDate: Type: string (date-time)

Date that this sequence source is released to be used to add versions of the same data
numberInSequence: Type: integer (int64)

Ordering of each Segment of the Component
position: Type: integer (int64)
startPosition: Type: integer (int64)

Start location of sequence
strand: Type: string

Strand Value

Nested Schema : OdbIdentifier

Type: object

Identifier assigned by a given system

Properties

system: Type: string

System which assigned this identifier
value: Type: string

Identifier value

400 Response

Invalid parameters supplied

404 Response

Genomic position(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/genes/50259/genomicPositions

Example of Response Body

The following example shows the contents of the response body in JSON format:

{
  "resourceType": "GenomicPositions",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "51649"
      },
      "genomicPosition": {
        "chromosome": "7",
        "startPosition": 55086714,
        "endPosition": 55324313,
        "strand": "+",
        "dnaReferenceVersion": "GRCH37.75"
      },
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/50259",
        "display": "EGFR"
      },
      "hugoName": "EGFR",
      "assembly": "GRCh37"
    }
  ],
  "count": 1,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/genes/50259/genomicPositions"
    }
  ]
}