Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Variants for Reference Identifiers and Database with GET Request

get

/ohfapi/cg/v3.3/variants/byReferenceId

This endpoint supports the retrieval of Variant Identifiers for multiple Reference Identifiers, multiple Database and single Assembly/Alignment ID.It also returns if any Invalid Reference Identifiers are passed in the Request.

Request

Supported Media Types

application/json
application/xml

Query Parameters

alignmentId: integer(int64)

Assembly/Alignment ID

database(optional): array

Collection Format: multi

Variant Reference Database

[0]: string

{
    "name":"database",
    "in":"query",
    "description":"Variant Reference Database",
    "required":false,
    "type":"array",
    "items":{
        "type":"string"
    },
    "collectionFormat":"multi"
}

limit(optional): integer(int32)

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

Row number to start from

referenceId: array

Collection Format: multi

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

Variant Reference ID

[0]: string

{
    "name":"referenceId",
    "in":"query",
    "description":"Variant Reference ID",
    "required":true,
    "type":"array",
    "items":{
        "type":"string"
    },
    "collectionFormat":"multi",
    "maxItems":2147483647,
    "minItems":1
}

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 : PageableDetailedCollection

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.
invalidAssemblies(optional): array invalidAssemblies

List of Invalid Assemblies in request.
invalidGeneNames(optional): array invalidGeneNames

List of Invalid Genenames in request.
invalidHugoNames(optional): array invalidHugoNames

List of Invalid Hugonames in request.
invalidReferenceIds(optional): array invalidReferenceIds

List of Invalid Reference IDs in request.
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/Serializable"
            }
        },
        "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"
            }
        },
        "invalidReferenceIds":{
            "type":"array",
            "description":"List of Invalid Reference IDs in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidHugoNames":{
            "type":"array",
            "description":"List of Invalid Hugonames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidGeneNames":{
            "type":"array",
            "description":"List of Invalid Genenames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidAssemblies":{
            "type":"array",
            "description":"List of Invalid Assemblies in request.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : invalidAssemblies

Type: array

List of Invalid Assemblies in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Assemblies in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidGeneNames

Type: array

List of Invalid Genenames in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Genenames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidHugoNames

Type: array

List of Invalid Hugonames in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Hugonames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidReferenceIds

Type: array

List of Invalid Reference IDs in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Reference IDs in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : items

Type: array

A collection of paged items.

Show Source

Array of: object Serializable

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

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 : Serializable

Type: object

400 Response

Assembly/Alignment Id is not supplied

404 Response

Variants not found for the Reference Ids and Reference Databases supplied

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&referenceId=rs142950474&referenceId=rs142950477&referenceId=COSM297314&referenceId=rs1&referenceId=COSM&database=dbSNP_138&database=COSMIC_COSMIC.V67&limit=2&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType" : "Variants",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "4754980"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "38063682"
    }
  } ],
  "count" : 2,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&referenceId=rs142950474&referenceId=rs142950477&referenceId=COSM297314&referenceId=rs1&referenceId=COSM&referenceId=dbSNP_138&referenceId=COSMIC_COSMIC.V67&limit=2&offset=0"
  }, {
    "rel" : "next",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&database=dbSNP_138&database=COSMIC_COSMIC.V67&offset=2&limit=2&referenceId=rs142950474&referenceId=rs142950477&referenceId=COSM297314&referenceId=rs1&referenceId=COSM"
  } ],
  "invalidReferenceIds" : [ "rs1", "COSM" ]
}