Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genesets

get

/ohfapi/cg/v3.3/geneSets

This endpoint supports the retrieval of Genesets by User Name. It returns Geneset information like Gene Set Identifier, Name, Description, Gene Count and other Geneset associated information.

Request

Supported Media Types

application/json
application/xml

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 : PageableCollectionGeneSet

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/GeneSet"
            }
        },
        "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 GeneSet

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

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 : GeneSet

Type: object

Show Source

geneCount(optional): object Number
geneSetDesc(optional): string

Gene Set Description. For ex.,RN5S300
geneSetId(optional): object Number
geneSetMember(optional): object LinkedReference
geneSetName(optional): string

Gene Set Name. For ex.,RN5S300
invalidGeneNames(optional): array invalidGeneNames

List of invalid Gene Names provided in the request
invalidHugoNames(optional): array invalidHugoNames

List of invalid HUGO Names provided in the request

{
    "type":"object",
    "properties":{
        "geneSetId":{
            "description":"Gene Set Identifier",
            "$ref":"#/definitions/Number"
        },
        "geneSetName":{
            "type":"string",
            "description":"Gene Set Name. For ex.,RN5S300"
        },
        "geneSetDesc":{
            "type":"string",
            "description":"Gene Set Description. For ex.,RN5S300"
        },
        "geneCount":{
            "description":"Total Number of Genes in Gene Set",
            "$ref":"#/definitions/Number"
        },
        "geneSetMember":{
            "example":"{href: 'geneSets/{geneSetId}'}",
            "description":"A link containing href to retrieve Geneset details",
            "$ref":"#/definitions/LinkedReference"
        },
        "invalidHugoNames":{
            "type":"array",
            "description":"List of invalid HUGO Names provided in the request",
            "items":{
                "type":"string"
            }
        },
        "invalidGeneNames":{
            "type":"array",
            "description":"List of invalid Gene Names provided in the request",
            "items":{
                "type":"string"
            }
        }
    }
}

Nested Schema : Number

Type: object

Nested Schema : LinkedReference

Type: object

Show Source

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

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

Nested Schema : invalidGeneNames

Type: array

List of invalid Gene Names provided in the request

Show Source

Array of: string

{
    "type":"array",
    "description":"List of invalid Gene Names provided in the request",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidHugoNames

Type: array

List of invalid HUGO Names provided in the request

Show Source

Array of: string

{
    "type":"array",
    "description":"List of invalid HUGO Names provided in the request",
    "items":{
        "type":"string"
    }
}

400 Response

Invalid parameters supplied

404 Response

geneSet(s) not found

Examples

The following example submits a GET request.

API URL

http:localhost:7010/ohfapi/cg/v3.3/geneSets?limit=10&offset=0

Example of Response Body

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

{
  "resourceType": "GeneSets",
  "items": [
    {
      "geneSetId": 7,
      "geneSetName": "GENE_SET7",
      "geneSetDesc": "GENE_SET_DESC7",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/7"
      }
    },
    {
      "geneSetId": 8,
      "geneSetName": "GENE_SET8",
      "geneSetDesc": "GENE_SET_DESC8",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/8"
      }
    },
    {
      "geneSetId": 9,
      "geneSetName": "GENE_SET9",
      "geneSetDesc": "GENE_SET_DESC9",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/9"
      }
    },
    {
      "geneSetId": 10,
      "geneSetName": "GENE_SET10",
      "geneSetDesc": "GENE_SET_DESC10",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/10"
      }
    },
    {
      "geneSetId": 11,
      "geneSetName": "GENE_SET11",
      "geneSetDesc": "GENE_SET_DESC11",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/11"
      }
    },
    {
      "geneSetId": 12,
      "geneSetName": "GENE_SET12",
      "geneSetDesc": "GENE_SET_DESC12",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/12"
      }
    },
    {
      "geneSetId": 13,
      "geneSetName": "GENE_SET13",
      "geneSetDesc": "GENE_SET_DESC13",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/13"
      }
    },
    {
      "geneSetId": 14,
      "geneSetName": "GENE_SET14",
      "geneSetDesc": "GENE_SET_DESC14",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/14"
      }
    },
    {
      "geneSetId": 15,
      "geneSetName": "GENE_SET15",
      "geneSetDesc": "GENE_SET_DESC15",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/15"
      }
    },
    {
      "geneSetId": 16,
      "geneSetName": "GENE_SET16",
      "geneSetDesc": "GENE_SET_DESC16",
      "geneCount": 10,
      "geneSetMember": {
        "reference": "/ohfapi/cg/v3.3/geneSets/16"
      }
    }
  ],
  "count": 10,
  "hasMore": true,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/geneSets?limit=10&offset=0"
    },
    {
      "rel": "next",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/geneSets?offset=10&limit=10"
    }
  ]
}