Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve misc_feature Components for a Gene Identifier

get

/ohfapi/cg/v3.3/genes/{id}/components/misc_feature

This endpoint supports the retrieval of misc_feature Components for a Gene Row ID passed. It returns all misc_feature Component information like Gene Name, Ensembl Version, Transcript Identifier, Component Name, Component Identifier, Genomic Positions, Strand and other misc_feature Component associated information. The 'Count' value displayed in the API represents the count of unique Gene Structure Identifiers

Request

Supported Media Types

application/json
application/xml

Path Parameters

id: integer(int64)

gene row ID

Query Parameters

limit(optional): integer(int32)

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

Row number to start from

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 : PageableCollectionGeneComponentSource

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/GeneComponentSource"
            }
        },
        "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 GeneComponentSource

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

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 : GeneComponentSource

Type: object

Show Source

componentSource(optional): object Transcript
ensemblVersion(optional): string

Ensembl Version. For ex.,GRCH37.75
geneName(optional): string

Gene Name. For ex.,RN5S300
geneReference(optional): object LinkedReference
identifier(optional): object Identifier

Identifier assigned by a given system

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Gene Component Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "geneName":{
            "type":"string",
            "description":"Gene Name. For ex.,RN5S300"
        },
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version. For ex.,GRCH37.75"
        },
        "componentSource":{
            "description":"Transcript Details",
            "$ref":"#/definitions/Transcript"
        },
        "geneReference":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Gene References details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : Transcript

Type: object

Show Source

componentTypes(optional): array componentTypes

List of Component Types
transcriptId(optional): string

Transcript ID

{
    "type":"object",
    "properties":{
        "transcriptId":{
            "type":"string",
            "description":"Transcript ID"
        },
        "componentTypes":{
            "type":"array",
            "description":"List of Component Types",
            "items":{
                "type":"string"
            }
        }
    }
}

Nested Schema : LinkedReference

Type: object

Show Source

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

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

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 : componentTypes

Type: array

List of Component Types

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Component Types",
    "items":{
        "type":"string"
    }
}

400 Response

Invalid parameters supplied

404 Response

Gene misc_feature component(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genes/50259/components/misc_feature

Example of Response Body

The following example shows the contents of the response body in JSON format:

 {
  "resourceType": "GeneComponents",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "225728"
      },
      "geneName": "ENSG00000146648",
      "ensemblVersion": "GRCH37.75",
      "componentSource": {
        "componentType": [
          {
            "componentName": "misc_feature",
            "componentId": 1193144,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55302533,
                "endPosition": 55302859,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193147,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55300931,
                "endPosition": 55301216,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193150,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55279147,
                "endPosition": 55279243,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193152,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55279028,
                "endPosition": 55279170,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193155,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55278846,
                "endPosition": 55278970,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193157,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55275980,
                "endPosition": 55276261,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193160,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55275586,
                "endPosition": 55275693,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
          {
            "componentName": "misc_feature",
            "componentId": 1193163,
            "genomicPosition": [
              {
                "chromosome": "7",
                "startPosition": 55275394,
                "endPosition": 55275702,
                "strand": "-",
                "numberInSequence": 1
              }
            ]
          },
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    }
  ],
  "count": 1,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genes/50259/components/misc_feature"
    }
  ]
}