Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Proteins for a Gene Identifier

get

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

This endpoint supports the retrieval of Proteins for a Gene Row ID passed. It returns Protein information like Protein Identifier, Name, Accession, Ensembl Version, Protein References and other Protein 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 : PageableCollectionGeneProtein

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/GeneProtein"
            }
        },
        "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 GeneProtein

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

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 : GeneProtein

Type: object

Show Source

accession(optional): string

Accession Identifier. For ex.,'P01308; Q5EEX2;'
ensemblVersion(optional): string

Ensembl Version. For ex.,GRCH37.75
geneReference(optional): object LinkedReference
proteinId(optional): integer(int64)

Protein Identifier
proteinName(optional): string

Name of Protein. For ex.,e.g. INS_HUMAN
proteinReferences(optional): array proteinReferences

List of Gene References

{
    "type":"object",
    "properties":{
        "proteinId":{
            "type":"integer",
            "format":"int64",
            "description":"Protein Identifier"
        },
        "proteinName":{
            "type":"string",
            "description":"Name of Protein. For ex.,e.g. INS_HUMAN"
        },
        "accession":{
            "type":"string",
            "description":"Accession Identifier. For ex.,'P01308; Q5EEX2;'"
        },
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version. For ex.,GRCH37.75"
        },
        "proteinReferences":{
            "type":"array",
            "description":"List of Gene References",
            "items":{
                "$ref":"#/definitions/GeneReference"
            }
        },
        "geneReference":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Gene References details",
            "$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"
        }
    }
}

Nested Schema : proteinReferences

Type: array

List of Gene References

Show Source

Array of: object GeneReference

{
    "type":"array",
    "description":"List of Gene References",
    "items":{
        "$ref":"#/definitions/GeneReference"
    }
}

Nested Schema : GeneReference

Type: object

Show Source

database(optional): string

Database Name. For ex.,dbSNP_142
dnaReferenceVersion(optional): string

Version Label. For ex.,SIFT_VER2_75
geneRef(optional): object LinkedReference
identifier(optional): object OdbIdentifier

Identifier assigned by a given system
referenceId(optional): string

Reference ID to External Database. For ex.,rs13079411

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Gene Set Identifier",
            "$ref":"#/definitions/OdbIdentifier"
        },
        "referenceId":{
            "type":"string",
            "description":"Reference ID to External Database. For ex.,rs13079411"
        },
        "database":{
            "type":"string",
            "description":"Database Name. For ex.,dbSNP_142"
        },
        "dnaReferenceVersion":{
            "type":"string",
            "description":"Version Label. For ex.,SIFT_VER2_75"
        },
        "geneRef":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Geneset details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : OdbIdentifier

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"
}

400 Response

Invalid parameters supplied

404 Response

Gene protein(s) not found

Examples

The following example submits a GET request.

API URL

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

Example of Response Body

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

{
  "resourceType": "Proteins",
  "items": [
    {
      "proteinId": 78371,
      "proteinName": "EGFR_HUMAN",
      "accession": "P00533; O00688; O00732; P06268; Q14225; Q68GS5; Q92795; Q9BZS2; Q9GZX1; Q9H2C9; Q9H3C9; Q9UMD7; Q9UMD8; Q9UMG5;",
      "ensemblVersion": "GRCH37.75",
      "proteinReferences": [
        {
          "referenceId": "ENSP00000275493",
          "database": "Ensembl"
        },
        {
          "referenceId": "X00588",
          "database": "EMBL"
        },
        {
          "referenceId": "U95089",
          "database": "EMBL"
        },
        {
          "referenceId": "U48722",
          "database": "EMBL"
        }  "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/proteins"
    }
  ]
}