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Retrieve Genes for Pathway Identifiers

get

/ohfapi/cg/v3.3/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: integer(int64)
  Minimum Value: 0

  Alignment row ID
• id: array
  Collection Format: multi

  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  List of Pathway row IDs

  • [0]: integer(int64)

  {
      "name":"id",
      "in":"query",
      "description":"List of Pathway row IDs",
      "required":true,
      "type":"array",
      "items":{
          "type":"integer",
          "format":"int64"
      },
      "collectionFormat":"multi",
      "maxItems":2147483647,
      "minItems":1
  }

• limit(optional): integer(int32)
  Number of rows to return
• offset(optional): integer(int32)
  Row number to start from

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollectionGene

Type: object

Model for paginated collections of data.

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• count(optional): integer(int64)
  Number of objects in the 'items' collection.
• hasMore(optional): boolean
  A boolean indicating if more pages are available.
• items(optional): array items
  A collection of paged items.
• links(optional): array links
  A collection of links containing hrefs to the current, next, and previous pages as applicable.
• resourceType(optional): string
  Identify the resource type

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string",
            "description":"Identify the resource type"
        },
        "items":{
            "type":"array",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/Gene"
            }
        },
        "count":{
            "type":"integer",
            "format":"int64",
            "description":"Number of objects in the 'items' collection."
        },
        "hasMore":{
            "type":"boolean",
            "description":"A boolean indicating if more pages are available."
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : items

Type: array

A collection of paged items.

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• Array of: object Gene

{
    "type":"array",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of paged items.",
    "items":{
        "$ref":"#/definitions/Gene"
    }
}

Nested Schema : links

Type: array

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

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• Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
    "items":{
        "type":"string"
    }
}

Example:

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

Nested Schema : Gene

Type: object

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• assembly(optional): string
  Assembly/Alignment Name. For ex.,GRCh38
• cancerGenes(optional): object LinkedReference
• chromosome(optional): string
  Chromosome Name. For ex.,'Y'
• chromosomeReference(optional): object LinkedReference
• description(optional): string
  Gene Description
• diseaseGenes(optional): object LinkedReference
• drugGenes(optional): object LinkedReference
• geneName(optional): string
  Gene Name. For ex.,RN5S300
• geneReference(optional): object LinkedReference
• geneXref(optional): object LinkedReference
• genomicPositions(optional): object LinkedReference
• hugoName(optional): string
  Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc.
• identifier(optional): object Identifier
  Identifier assigned by a given system
• pathways(optional): object LinkedReference
• resourceType(optional): string
• transcripts(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string"
        },
        "identifier":{
            "description":"Gene Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "geneName":{
            "type":"string",
            "description":"Gene Name. For ex.,RN5S300"
        },
        "hugoName":{
            "type":"string",
            "description":"Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc. "
        },
        "assembly":{
            "type":"string",
            "description":"Assembly/Alignment Name. For ex.,GRCh38"
        },
        "chromosomeReference":{
            "$ref":"#/definitions/LinkedReference"
        },
        "chromosome":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "geneReference":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Gene details",
            "$ref":"#/definitions/LinkedReference"
        },
        "description":{
            "type":"string",
            "description":"Gene Description"
        },
        "genomicPositions":{
            "example":"{href: '/genes/{geneId}/genomicPositions'}",
            "description":"A link containing href to retrieve Gene Genomic Position details",
            "$ref":"#/definitions/LinkedReference"
        },
        "transcripts":{
            "example":"{href: '/genes/{geneId}/transcripts'}",
            "description":"A link containing href to retrieve Gene Transcipt details",
            "$ref":"#/definitions/LinkedReference"
        },
        "pathways":{
            "example":"{href: '/genes/{geneId}/pathways'}",
            "description":"A link containing href to retrieve Gene Pathway details",
            "$ref":"#/definitions/LinkedReference"
        },
        "diseaseGenes":{
            "example":"{href: '/genes/{geneId}/diseases'}",
            "description":"A link containing href to retrieve Gene Disease details",
            "$ref":"#/definitions/LinkedReference"
        },
        "drugGenes":{
            "example":"{href: '/genes/{geneId}/drugs'}",
            "description":"A link containing href to retrieve Gene Drug details",
            "$ref":"#/definitions/LinkedReference"
        },
        "cancerGenes":{
            "example":"{href: '/genes/{geneId}/cancer'}",
            "description":"A link containing href to retrieve Gene Cancer details",
            "$ref":"#/definitions/LinkedReference"
        },
        "geneXref":{
            "example":"{href: '/genes/{geneId}/geneXref'}",
            "description":"A link containing href to retrieve Gene Xref details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : LinkedReference

Type: object

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• display(optional): string
• reference(optional): string

{
    "type":"object",
    "properties":{
        "reference":{
            "type":"string"
        },
        "display":{
            "type":"string"
        }
    }
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

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• system(optional): string
  System which assigned this identifier
• value(optional): string
  Identifier value

{
    "type":"object",
    "properties":{
        "system":{
            "type":"string",
            "description":"System which assigned this identifier"
        },
        "value":{
            "type":"string",
            "description":"Identifier value"
        }
    },
    "description":"Identifier assigned by a given system"
}

400 Response

Invalid parameters supplied

404 Response

Genes(s) not found

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/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": "/ohfapi/cg/v3.3/genes/77"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "231"
      },
      "geneName": "ENSG00000116251",
      "hugoName": "RPL22",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/231"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "693"
      },
      "geneName": "ENSG00000070831",
      "hugoName": "CDC42",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/693"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "706"
      },
      "geneName": "ENSG00000133216",
      "hugoName": "EPHB2",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/706"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "927"
      },
      "geneName": "ENSG00000130772",
      "hugoName": "MED18",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/927"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "1115"
      },
      "geneName": "ENSG00000126067",
      "hugoName": "PSMB2",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/1115"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "1322"
      },
      "geneName": "ENSG00000159479",
      "hugoName": "MED8",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/1322"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "2174"
      },
      "geneName": "ENSG00000122406",
      "hugoName": "RPL5",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/2174"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "2425"
      },
      "geneName": "ENSG00000143106",
      "hugoName": "PSMA5",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/2425"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "2590"
      },
      "geneName": "ENSG00000134259",
      "hugoName": "NGF",
      "assembly": "GRCh37",
      "chromosome": "1",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/2590"
      }
    }
  ],
  "count": 10,
  "hasMore": true,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genes/byPathway?id=12&id=13&alignmentId=1&limit=10&offset=0"
    },
    {
      "rel": "next",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genes/byPathway?alignmentId=1&offset=10&limit=10&id=12&id=13"
    }
  ]
}

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