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Retrieve Variants for Variant Effect and Gene Identifiers

get

/ohfapi/cg/v3.3/variants/byEffect/byGenewid

This endpoint supports the retrieval of Variant Identifiers for Variant Effect, multiple Gene Identifiers and Assembly/Alignment Identifier.

Request

Supported Media Types

• application/json
• application/xml

Query Parameters

• alignmentId: integer(int64)
  Minimum Value: 0

  Assembly/Alignment ID
• geneWid: array
  Collection Format: multi

  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  Gene ID

  • [0]: integer(int64)

  {
      "name":"geneWid",
      "in":"query",
      "description":"Gene ID",
      "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
• variantEffect: string
  Variant Effect

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollectionVariant

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/Variant"
            }
        },
        "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 Variant

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

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 : Variant

Type: object

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• identifier(optional): object Identifier
  Identifier assigned by a given system
• variantPrediction(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Variant Row ID",
            "$ref":"#/definitions/Identifier"
        },
        "variantPrediction":{
            "example":"{href: '/variants/{variantRecordId}/variantPredictions'}",
            "description":"A link containing href to retrieve Variant Prediction details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

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"
}

Nested Schema : LinkedReference

Type: object

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

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

400 Response

Filter Variants input is not valid

404 Response

Variants not found for the Gene Wids and VariantEffect supplied

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byEffect/byGenewid?geneWid=6280&geneWid=123&variantEffect=synonymous&alignmentId=1&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType" : "Variants",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "27423"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "34705850"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "34705852"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "34705854"
    }
  } ],
  "count" : 4,
  "hasMore" : false,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byEffect/byGenewid?geneWid=6280&geneWid=123&variantEffect=synonymous&alignmentId=1&limit=10&offset=0"
  } ]
}

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