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Retrieve Genomic Positions for Gene Identifiers

get

/ohfapi/cg/v3.3/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: array
  Collection Format: multi

  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  Genes row IDs

  • [0]: integer(int64)

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

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

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollectionGenePosition

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/GenePosition"
            }
        },
        "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.

Show Source

• Array of: object GenePosition

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

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 : GenePosition

Type: object

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• assembly(optional): string
  Assembly/Alignment Name. For ex.,GRCh38
• geneReference(optional): object LinkedReference
• genomicPosition(optional): object GenomicPosition
• 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 OdbIdentifier
  Identifier assigned by a given system

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Gene Identifier",
            "$ref":"#/definitions/OdbIdentifier"
        },
        "genomicPosition":{
            "description":"Genomic Position Details",
            "$ref":"#/definitions/GenomicPosition"
        },
        "geneReference":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Gene References details",
            "$ref":"#/definitions/LinkedReference"
        },
        "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"
        }
    }
}

Nested Schema : LinkedReference

Type: object

Show Source

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

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

Nested Schema : GenomicPosition

Type: object

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• chromosome(optional): string
  Chromosome Name. For ex.,'Y'
• chromosomeId(optional): string
• chromosomeName(optional): string
  Chromosome Name. For ex.,'Y'
• dateOfLoading(optional): string(date-time)
  Insert Date
• dnaReferenceVersion(optional): string
  Version Label. For ex.,SIFT_VER2_75
• endPosition(optional): integer(int64)
  End location of sequence
• ensemblReleaseDate(optional): string(date-time)
  Date that this sequence source is released to be used to add versions of the same data
• numberInSequence(optional): integer(int64)
  Ordering of each Segment of the Component
• position(optional): integer(int64)
• startPosition(optional): integer(int64)
  Start location of sequence
• strand(optional): string
  Strand Value

{
    "type":"object",
    "properties":{
        "chromosomeId":{
            "type":"string"
        },
        "chromosomeName":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "chromosome":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "position":{
            "type":"integer",
            "format":"int64"
        },
        "startPosition":{
            "type":"integer",
            "format":"int64",
            "description":"Start location of sequence"
        },
        "endPosition":{
            "type":"integer",
            "format":"int64",
            "description":"End location of sequence"
        },
        "dateOfLoading":{
            "type":"string",
            "format":"date-time",
            "description":"Insert Date"
        },
        "strand":{
            "type":"string",
            "description":"Strand Value"
        },
        "dnaReferenceVersion":{
            "type":"string",
            "description":"Version Label. For ex.,SIFT_VER2_75"
        },
        "numberInSequence":{
            "type":"integer",
            "format":"int64",
            "description":"Ordering of each Segment of the Component"
        },
        "ensemblReleaseDate":{
            "type":"string",
            "format":"date-time",
            "description":"Date that this sequence source is released to be used to add versions of the same data"
        }
    }
}

Nested Schema : OdbIdentifier

Type: object

Identifier assigned by a given system

Show Source

• 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

Gene genomic position(s) not found

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Examples

The following example submits a GET request.

API URL

http://localhost:port/ohfapi/cg/v3.3/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" : "/ohfapi/cg/v3.3/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" : "/ohfapi/cg/v3.3/genes/23472",
      "display" : "Y_RNA"
    },
    "hugoName" : "Y_RNA",
    "assembly" : "GRCh37"
  } ],
  "count" : 2,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/genes/genomicPositions?id=23472&id=23475&limit=20&offset=0"
  }, {
    "rel" : "next",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/genes/genomicPositions?offset=20&limit=20&id=23472&id=23475"
  } ]
}

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