Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Variants for Variant Effect and Chromosome

get

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

This endpoint supports the retrieval of Variant Identifiers for Variant Effect, Chromosome, Start Position, End Position and Assembly/Alignment Identifier.

Request

Supported Media Types

application/json
application/xml

Query Parameters

alignmentId: integer(int64)

Assembly/Alignment ID
chromosome: string

Chromosome Name. For ex.,'Y'
endPosition: integer(int64)

Chromosome End Position
limit(optional): integer(int32)

Number of rows to return
offset(optional): integer(int32)

Row number to start from
startPosition: integer(int64)

Start location of sequence
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 Chromosome and VariantEffect supplied

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byEffect/byChromosome?alignmentId=1&chromosome=CHR&startPosition=10250&endPosition=10251&variantEffect=synonymous&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "items":[
  {
  "identifier":"138260072"
  }
  ]
  "count": 1,
  "hasMore": false,
  "links" : [ {
     "rel" : "self",
     "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byEffect/byChromosome?alignmentId=1&chromosome=CHR&startPosition=10250&endPosition=10251&variantEffect=synonymous&limit=10&offset=0"
   } ] 
}