Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Variants for Prediction and Chromosome

get

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

This endpoint supports the retrieval of Variant Identifiers for Chromosome, Start Position, End Position, Assembly/Alignment Identifier, Prediction Type, multiple Prediction Code, Prediction Score and Prediction Comparator. The response fetches Variants Identifiers which are having defined prediction code or score. Both SIFT and PolyPhen (Polymorphism Phenotyping) type data can be searched using this API.

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

predictionCode(optional): array

Collection Format: multi

List of Prediction Codes. For ex.,deleterious

[0]: string

{
    "name":"predictionCode",
    "in":"query",
    "description":"List of Prediction Codes. For ex.,deleterious",
    "required":false,
    "type":"array",
    "items":{
        "type":"string"
    },
    "collectionFormat":"multi"
}

predictionComparator(optional): string

Prediction Score Comparator( < , > , = )
predictionScore(optional): string

Prediction Score .For ex.,1
predictionType: string

Prediction Type. for ex.,SIFT
startPosition: integer(int64)

Start location of sequence

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

Chromosome End Position is not supplied

404 Response

Variants not found for the Chromosome and Prediction details supplied

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byPrediction/byChromosome?chromosome=CHR&startPosition=10250&endPosition=10251&predictionType=SIFT&predictionScore=1&predictionComparator=<&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":"536778"
         },
         "variantPrediction":{
            "reference":"/ohfapi/cg/v3.3/variants/536778/variantPredictions"
         }
      },
      {
         "identifier":{
            "system":"ODB",
            "value":"536777"
         },
         "variantPrediction":{
            "reference":"/ohfapi/cg/v3.3/variants/536777/variantPredictions"
         }
      }
   ],
   "count":2,
   "hasMore":false,
   "links":[
      {
         "rel":"self",
         "href":"http://localhost:7010/ohfapi/cg/v3.3/variants/byPrediction/byChromosome?chromosome=CHR&startPosition=10250&endPosition=10251&predictionType=SIFT&predictionScore=1&predictionComparator=<&alignmentId=1&limit=10&offset=0"
      }
   ]
}