REST API for Oracle Healthcare Translational Research

Retrieve Genomic Positions for Gene Identifiers

get

/HSDataService-web/api/3.2.0/genes/genomicPositions

This endpoint supports the retrieval of Genomic Positions for multiple Gene Row IDs 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

Query Parameters

id

Type: array

Required: true

Collection Format: multi

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

Genes row IDs

Items

Type: integer (int64)

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

Gene genomic position(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:port/HSDataService-web/api/3.2.0/genes/genomicPositions?id=23472&id=23475&limit=20&offset=0

Example of Response Body

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

{
    "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "24087"
    },
    "genomicPosition" : {
      "chromosome" : "12",
      "startPosition" : 2969115,
      "endPosition" : 2969199,
      "strand" : "+",
      "dnaReferenceVersion" : "GRCH37.75"
    },
    "geneReference" : {
      "reference" : "/HSDataService-web/api/3.2.0/genes/23472",
      "display" : "Y_RNA"
    },
    "hugoName" : "Y_RNA",
    "assembly" : "GRCh37"
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "24162"
    },
    "genomicPosition" : {
      "chromosome" : "12",
      "startPosition" : 6343511,
      "endPosition" : 6343621,
      "strand" : "-",
      "dnaReferenceVersion" : "GRCH37.75"
    },
    "geneReference" : {
      "reference" : "/HSDataService-web/api/3.2.0/genes/23472",
      "display" : "Y_RNA"
    },
    "hugoName" : "Y_RNA",
    "assembly" : "GRCh37"
  } ],
  "count" : 2,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7001/HSDataService-web/api/3.2.0/genes/genomicPositions?id=23472&id=23475&limit=20&offset=0"
  }, {
    "rel" : "next",
    "href" : "http://localhost:7001/HSDataService-web/api/3.2.0/genes/genomicPositions?offset=20&limit=20&id=23472&id=23475"
  } ]
}