Clinical Genomic APIs for Oracle Healthcare Foundation

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)

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

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Model for paginated collections of data.

Root Schema : PageableCollectionVariant

Type: object

Model for paginated collections of data.

Show Source

count(optional): integer(int64)

Number of objects in the 'items' collection.
hasMore(optional): boolean

Default Value: false

A boolean indicating if more pages are available.
items(optional): array items

A collection of paged items.
links(optional): array link

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":{
                "name":"items",
                "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.",
            "default":false
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "name":"link",
                "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 Variant

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

Nested Schema : link

Type: array

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

Show Source

Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "name":"link",
        "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

Show Source

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

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"
}

Nested Schema : LinkedReference

Type: object

Show Source

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

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"
  } ]
}