Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Diseases for a Gene Identifier

get

/ohfapi/cg/v3.3/genes/{id}/diseases

This endpoint supports the retrieval of Diseases for a Gene Row ID passed. It returns Disease information like Disease Name, Mutation Type, Curation Source, Confidence and other Disease associated information.

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 : PageableCollectionDisease

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/Disease"
            }
        },
        "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 Disease

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

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 : Disease

Type: object

Show Source

assembly(optional): string

Assembly NameAssembly/Alignment Name. For ex.,GRCh38
confidence(optional): string

Confidence
curationSource(optional): string

Curation Source
diseaseName(optional): string

Disease Name
ensemblVersion(optional): string

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

Feature
geneRef(optional): object LinkedReference
mutationType(optional): string

Mutation Type
variantReferences(optional): object LinkedReference
variantType(optional): string

Variant Type

{
    "type":"object",
    "properties":{
        "diseaseName":{
            "type":"string",
            "description":"Disease Name"
        },
        "mutationType":{
            "type":"string",
            "description":"Mutation Type"
        },
        "variantType":{
            "type":"string",
            "description":"Variant Type"
        },
        "feature":{
            "type":"string",
            "description":"Feature"
        },
        "confidence":{
            "type":"string",
            "description":"Confidence"
        },
        "curationSource":{
            "type":"string",
            "description":"Curation Source"
        },
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version. For ex.,GRCH37.75"
        },
        "assembly":{
            "type":"string",
            "description":"Assembly NameAssembly/Alignment Name. For ex.,GRCh38"
        },
        "geneRef":{
            "$ref":"#/definitions/LinkedReference"
        },
        "variantReferences":{
            "example":"{href: '/variants/{variantRecordId}'}",
            "description":"A link containing href to retrieve Variant Annotation details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : LinkedReference

Type: object

Show Source

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

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

400 Response

Invalid parameters supplied

404 Response

Disease(s) not found

Examples

The following example submits a GET request.

API URL

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

Example of Response Body

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

{
  "resourceType": "DiseaseGenes",
  "items": [
    {
      "diseaseName": "Squamous cell carcinoma of head & neck",
      "mutationType": "M",
      "variantType": "DM?",
      "confidence": "Low",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Breast cancer%2C association with",
      "mutationType": "M",
      "variantType": "DP",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Lung cancer%2C association with",
      "mutationType": "M,E",
      "variantType": "DP",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Glioblastoma%2C risk%2C association with",
      "mutationType": "R",
      "variantType": "DFP",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Lung cancer%2C susceptibility to",
      "mutationType": "M",
      "variantType": "DM",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Altered transmembrane signaling",
      "mutationType": "M",
      "variantType": "DFP",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Lung cancer",
      "mutationType": "M",
      "variantType": "DM,DM?",
      "confidence": "High,Low",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Bladder cancer%2C association with",
      "mutationType": "R",
      "variantType": "DFP",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    },
    {
      "diseaseName": "Reduced transcription",
      "mutationType": "E",
      "variantType": "FP",
      "confidence": "High",
      "curationSource": "BIOBASE",
      "ensemblVersion": "GRCH37.75",
      "geneRef": {
        "reference": "/ohfapi/cg/v3.3/genes/50259"
      }
    }
  ],
  "count": 9,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genes/50259/diseases"
    }
  ]
}