Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genomics Specimen Identifiers for Clinical Specimen Identifiers

get

/ohfapi/cg/v3.3/{apiContext}/clinicalspecimens/genomicspecimens

This endpoint supports the retrieval of Patient/Subject Genomic Specimen Row IDs List for multiple Clinical Specimens Row IDs, if Clinical Specimen is valid and has corresponding omics data.

Request

Supported Media Types

application/json
application/xml

Path Parameters

apiContext: string

Pattern: subjectapi|patientapi

Patient/Subject API context

Query Parameters

id: array

Collection Format: multi

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

Patient/Subject Clinical Specimen Row IDs List

[0]: integer(int64)

{
    "name":"id",
    "in":"query",
    "description":"Patient/Subject Clinical Specimen Row IDs List",
    "required":true,
    "type":"array",
    "items":{
        "type":"integer",
        "format":"int64"
    },
    "collectionFormat":"multi",
    "maxItems":2147483647,
    "minItems":1
}

limit(optional): integer(int32)

Pagination query params: ?limit=2&offset=0
offset(optional): integer(int32)

Pagination query params: ?limit=2&offset=0

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 : PageableCollectionGenomicSpecimen

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/GenomicSpecimen"
            }
        },
        "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 GenomicSpecimen

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

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 : GenomicSpecimen

Type: object

Show Source

genomicFileMetadata(optional): object LinkedReference
genomicSpecimenMetadata(optional): object LinkedReference
identifier(optional): object Identifier

Identifier assigned by a given system
patient(optional): object LinkedReference
resourceType(optional): string
specimenNumber(optional): string

Specimen identifier in linked Specimen Datasource Database
specimenVendorNumber(optional): string

Vendor Identifier in linked Specimen Datasource Database
subject(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string"
        },
        "identifier":{
            "description":"Genomic Specimen Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "specimenNumber":{
            "type":"string",
            "description":"Specimen identifier in linked Specimen Datasource Database"
        },
        "specimenVendorNumber":{
            "type":"string",
            "description":"Vendor Identifier in linked Specimen Datasource Database"
        },
        "genomicSpecimenMetadata":{
            "example":"{href: 'patientapi/genomicspecimens/{id}/metadata'}",
            "description":"A link containing href to retrieve Genomic Specimen Metadata details",
            "$ref":"#/definitions/LinkedReference"
        },
        "genomicFileMetadata":{
            "example":"{href: 'patientapi/genomicspecimens/{id}/fileMetadata'}",
            "description":"A link containing href to retrieve Genomic Specimen File Metadata details",
            "$ref":"#/definitions/LinkedReference"
        },
        "subject":{
            "$ref":"#/definitions/LinkedReference"
        },
        "patient":{
            "$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 : 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"
}

400 Response

Invalid parameters supplied

404 Response

Genomic specimen or genomic specimen metadata not found

Examples

The following example submits a GET request.

API URL ??? Patient Context

http://localhost:7010/ohfapi/cg/v3.3/patientapi/clinicalspecimens/genomicspecimens?id=96&id=97&limit=20&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "GenomicSpecimen",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "71"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/97"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "63"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/96"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://loalhost:7010/ohfapi/cg/v3.3/patientapi/clinicalspecimens/genomicspecimens?id=96&id=97&limit=20&offset=0"
    }
  ]
}

API URL ??? Subject Context

http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/genomicspecimens?id=96&id=97&limit=20&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "GenomicSpecimen",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "63"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/96"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "71"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/97"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/genomicspecimens?id=96&id=97&limit=20&offset=0"
    }
  ]
}