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Retrieve Genomic Specimen details for a Clinical Specimen Identifier

get

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

This endpoint supports the retrieval of Genomic Specimen for a single Clinical Specimen Identifier passed. It returns Genomic Specimen information like Specimen Number, Specimen Vendor Number and other Genomic Specimen associated information.

Request

Supported Media Types

• application/json
• application/xml

Path Parameters

• apiContext: string
  Pattern: patientapi|subjectapi
• id: integer(int64)
  Minimum Value: 0

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root 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 request parameters

404 Response

Query status not found

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Examples

The following example submits a GET request.

API URL ??? Patient Context

http://localhost:7010/ohfapi/cg/v3.3/patientapi/genomicspecimens/10096?limit=20&offset=0

Example of Response Body

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

{
  "resourceType": "GenomicSpecimen",
  "identifier": {
    "system": "ODB",
    "value": "63"
  },
  "specimenNumber": "HG000_10096",
  "specimenVendorNumber": "vendor2",
  "genomicSpecimenMetadata": {
    "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/63/metadata"
  },
  "genomicFileMetadata": {
    "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/63/fileMetadata"
  },
  "patient": {
    "reference": "/ohfapi/cg/v3.3/patientapi/patients/2"
  }
}

API URL ??? Subject Context

http://localhost:7010/ohfapi/cg/v3.3/subjectapi/genomicspecimens/1

Example of Response Body

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

{
  "resourceType": "GenomicSpecimen",
  "identifier": {
    "system": "ODB",
    "value": "40001"
  },
  "specimenNumber": "ADME_SPEC1",
  "specimenVendorNumber": "adme",
  "genomicSpecimenMetadata": {
    "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40001/metadata"
  },
  "genomicFileMetadata": {
    "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40001/fileMetadata"
  },
  "subject": {
    "reference": "/ohfapi/cg/v3.3/subjectapi/subjects/7"
  }
}

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