REST API for Oracle Healthcare Translational Research

Retrieve Genes for Pathway Identifiers

get

/HSDataService-web/api/3.2.0/genes/byPathway

This endpoint supports the retrieval of Genes for multiple Pathway Row IDs and Assembly/Alignment Row ID passed. It returns Gene information like Gene Name, HUGO Name, Assembly/Alignment, Chromosome and other Gene related information.

Request

Supported Media Types

application/json
application/xml

Query Parameters

alignmentId

Type: integer (int64)

Required: true

Alignment row ID

id

Type: array

Required: true

Collection Format: multi

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

List of Pathway row IDs

Items

Type: integer (int64)

limit

Type: integer (int32)

Number of rows to return

offset

Type: integer (int32)

Row number to start from

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Model for paginated collections of data.

Root Schema : PageableCollectionGene

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 Gene

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 : Gene

Type: object

Properties

assembly: Type: string

Assembly/Alignment Name. For ex.,GRCh38
cancerGenes: Type: object LinkedReference
chromosome: Type: string

Chromosome Name. For ex.,'Y'
chromosomeReference: Type: object LinkedReference
description: Type: string

Gene Description
diseaseGenes: Type: object LinkedReference
drugGenes: Type: object LinkedReference
geneName: Type: string

Gene Name. For ex.,RN5S300
geneReference: Type: object LinkedReference
geneXref: Type: object LinkedReference
genomicPositions: Type: object LinkedReference
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 Identifier

Identifier assigned by a given system
pathways: Type: object LinkedReference
resourceType: Type: string
transcripts: Type: object LinkedReference

Nested Schema : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

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

400 Response

Invalid parameters supplied

404 Response

Genes(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/genes/byPathway?id=12&id=13&alignmentId=1&limit=10&offset=0

Example of Response Body

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

{
  "resourceType": "Genes",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "77"
      },
      "geneName": "ENSG00000188157",
      "hugoName": "AGRN",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/77"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "231"
      },
      "geneName": "ENSG00000116251",
      "hugoName": "RPL22",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/231"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "693"
      },
      "geneName": "ENSG00000070831",
      "hugoName": "CDC42",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/693"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "706"
      },
      "geneName": "ENSG00000133216",
      "hugoName": "EPHB2",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/706"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "927"
      },
      "geneName": "ENSG00000130772",
      "hugoName": "MED18",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/927"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "1115"
      },
      "geneName": "ENSG00000126067",
      "hugoName": "PSMB2",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/1115"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "1322"
      },
      "geneName": "ENSG00000159479",
      "hugoName": "MED8",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/1322"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "2174"
      },
      "geneName": "ENSG00000122406",
      "hugoName": "RPL5",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/2174"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "2425"
      },
      "geneName": "ENSG00000143106",
      "hugoName": "PSMA5",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/2425"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "2590"
      },
      "geneName": "ENSG00000134259",
      "hugoName": "NGF",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/HSDataService-web/api/3.2.0/genes/2590"
      }
    }
  ],
  "count": 10,
  "hasMore": true,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/genes/byPathway?id=12&id=13&alignmentId=1&limit=10&offset=0"
    },
    {
      "rel": "next",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/genes/byPathway?alignmentId=1&offset=10&limit=10&id=12&id=13"
    }
  ]
}