REST API for Oracle Healthcare Translational Research

Retrieve Clinical Specimen for Specimen Identifiers

get

/HSDataService-web/api/3.2.0/{apiContext}/clinicalspecimens

This endpoint supports the retrieval of a Paginated List of Clinical Specimens for none or multiple Clinical Specimen row IDs. It returns Clinical Specimens information like Clinical Specimen Status, Type, Subtype, Number, Accession Identifier or Specimen Number, Specimen Vendor Number, Collection details including Collection date/time, Collection method, Collection anatomical site and Collection quantity, Clinical Specimen Size, Weight, Cut Thickness and some other Clinical Specimen associated information.

Request

Supported Media Types

application/json
application/xml

Path Parameters

apiContext: Type: string

Required: true

Pattern: subjectapi|patientapi

Patient/Subject API context

Query Parameters

id

Type: array

Collection Format: multi

Patient/Subject Clinical Specimen Row IDs

Items

Type: integer (int64)

limit

Type: integer (int32)

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

offset

Type: integer (int32)

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

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Model for paginated collections of data.

Root Schema : PageableCollectionClinicalSpecimen

Type: object

Model for paginated collections of data.

Properties

count: Type: integer (int64)

Number of objects in the 'items' collection.
hasMore: Type: boolean

Default Value: false

A boolean indicating if more pages are available.
items: Type: array items

A collection of paged items.
links: Type: array links

A collection of links containing hrefs to the current, next, and previous pages as applicable.
resourceType: Type: string

Identify the resource type

Nested Schema : items

Type: array

A collection of paged items.

Items

Type: object ClinicalSpecimen

Model for a Clinical Specimen object in CDM.

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

Example

{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}

Items

Type: string

Nested Schema : ClinicalSpecimen

Type: object

Model for a Clinical Specimen object in CDM.

Properties

accessionIdentifier: Type: string

The Clinical Specimen identifier.
collection: Type: object Collection

Model for a Clinical Specimen Collection details object in CDM.
cutThicknessUnitOfMeasure: Type: object Coding

Model for a reference to a code defined by a terminology system.
expirationDate: Type: string (date-time)

The Clinical Specimen expiration date and time.
identifier: Type: object Identifier

Identifier assigned by a given system
maximumCutThickness: Type: string

The Clinical Specimen maximum Cut Thickness.
mininumCutThickness: Type: string

The Clinical Specimen mininum Cut Thickness.
patient: Type: object LinkedReference
receivedDate: Type: string (date-time)

The Clinical Specimen received date and time.
resourceType: Type: string

API resource type. it's included if Response is not paginated.
sentDate: Type: string (date-time)

The Clinical Specimen sent date and time.
sizeUnitOfMeasure: Type: object Coding

Model for a reference to a code defined by a terminology system.
specimenFinalWeight: Type: string

The Clinical Specimen Final Weight.
specimenHeight: Type: string

The Clinical Specimen Height.
specimenInitialWeight: Type: string

The Clinical Specimen Initial Weight.
specimenIntermediateWeight: Type: string

The Clinical Specimen Intermediate Weight.
specimenLength: Type: string

The Clinical Specimen Length.
specimenVendorNumber: Type: string

The Clinical Specimen Vendor identifier.
specimenWidth: Type: string

The Clinical Specimen Width.
status: Type: object Coding

Model for a reference to a code defined by a terminology system.
subject: Type: object LinkedReference
subtype: Type: object CodeableConcept

Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
type: Type: object CodeableConcept

Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
weightUnitOfMeasure: Type: object Coding

Model for a reference to a code defined by a terminology system.

Nested Schema : Collection

Type: object

Model for a Clinical Specimen Collection details object in CDM.

Properties

bodySite: Type: object CodeableConcept

Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
collectedDateTime: Type: string (date-time)

The Clinical Specimen collection date and time.
method: Type: object Coding

Model for a reference to a code defined by a terminology system.
quantity: Type: object Quantity

Model for a Quantity object in CDM.

Nested Schema : Coding

Type: object

Model for a reference to a code defined by a terminology system.

Properties

code: Type: string

Symbol in syntax defined by the system.
description: Type: string

Description defined by the system.
display: Type: string

Representation defined by the system.
sysId: Type: string

Identity of the terminology system.
sysName: Type: string

Name of the terminology system.
sysVersion: Type: string

Version of the system - if relevant.

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

Properties

system: Type: string

System which assigned this identifier
value: Type: string

Identifier value

Nested Schema : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

Nested Schema : CodeableConcept

Type: object

Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.

Properties

coding: Type: array coding

Read Only: true

Code(s) defined by a terminology system.
text: Type: string

Plain text representation of the concept.

Nested Schema : Quantity

Type: object

Model for a Quantity object in CDM.

Properties

code: Type: string

The quantity units symbol in syntax defined by the system.
description: Type: string

The quantity units description.
sysId: Type: string

The quantity units terminology system identifier.
sysName: Type: string

The quantity units terminology system name.
sysVersion: Type: string

The quantity units terminology system version.
units: Type: string

The quantity units displayable name.
value: Type: string

The numerical value of the quantity.

Nested Schema : coding

Type: array

Read Only: true

Code(s) defined by a terminology system.

Items

Type: object Coding

Model for a reference to a code defined by a terminology system.

400 Response

Invalid parameters supplied

404 Response

Specimen(s) not found

Examples

The following example submits a GET request.

API URL — Subject Context

http://localhost:7001/HSDataService-web/api/3.2.0/subjectapi/clinicalspecimens?id=1&id=2

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "Specimen",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "1"
      },
      "status": {
        "code": "1",
        "display": "N/A1"
      },
      "type": {
        "coding": [
          {
            "code": "1",
            "display": "SP1",
            "description": "SP1Name",
            "sysId": "EHA_CUSTOM_CD_SYS",
            "sysName": "EHA Custom Code System",
            "sysVersion": "1"
          }
        ]
      },
      "subtype": {
        "coding": [
          {
            "code": "1",
            "display": "N/A1"
          }
        ]
      },
      "accessionIdentifier": "HG000_1",
      "specimenVendorNumber": "vendor2",
      "collection": {
        "collectedDateTime": "01/01/1998",
        "method": {
          "code": "1",
          "display": "N/A1"
        },
        "bodySite": {
          "coding": [
            {
              "code": "ANA_SITE_CD_CODE1",
              "display": "ANA_SITE_CD_CODE1name",
              "description": "ANA_SITE_CD_CODE1Desc",
              "sysId": "EHA_CUSTOM_CD_SYS",
              "sysName": "EHA Custom Code System",
              "sysVersion": "1"
            }
          ]
        },
        "quantity": {
          "value": "50",
          "units": "cm",
          "code": "1",
          "description": "centi meter",
          "sysId": "1",
          "sysName": "UOM code",
          "sysVersion": "UOM version"
        }
      },
      "specimenLength": "0.2",
      "specimenWidth": "0.1",
      "specimenHeight": "0.05",
      "sizeUnitOfMeasure": {
        "code": "1",
        "display": "cm",
        "description": "centi meter",
        "sysId": "1",
        "sysName": "UOM code",
        "sysVersion": "UOM version"
      },
      "mininumCutThickness": "0.0005",
      "maximumCutThickness": "0.0008",
      "cutThicknessUnitOfMeasure": {
        "code": "1",
        "display": "cm",
        "description": "centi meter",
        "sysId": "1",
        "sysName": "UOM code",
        "sysVersion": "UOM version"
      },
      "specimenInitialWeight": "0.005",
      "specimenIntermediateWeight": "0.003",
      "specimenFinalWeight": "0.001",
      "weightUnitOfMeasure": {
        "code": "1",
        "display": "cm",
        "description": "centi meter",
        "sysId": "1",
        "sysName": "UOM code",
        "sysVersion": "UOM version"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/subjects/1"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "2"
      },
      "status": {
        "code": "1",
        "display": "N/A1"
      },
      "type": {
        "coding": [
          {
            "code": "2",
            "display": "SP2",
            "description": "SP2Name",
            "sysId": "EHA_CUSTOM_CD_SYS",
            "sysName": "EHA Custom Code System",
            "sysVersion": "1"
          }
        ]
      },
      "subtype": {
        "coding": [
          {
            "code": "1",
            "display": "N/A1"
          }
        ]
      },
      "accessionIdentifier": "HG000_2",
      "specimenVendorNumber": "vendor2",
      "collection": {
        "collectedDateTime": "01/01/1998",
        "method": {
          "code": "1",
          "display": "N/A1"
        },
        "bodySite": {
          "coding": [
            {
              "code": "ANA_SITE_CD_CODE1",
              "display": "ANA_SITE_CD_CODE1name",
              "description": "ANA_SITE_CD_CODE1Desc",
              "sysId": "EHA_CUSTOM_CD_SYS",
              "sysName": "EHA Custom Code System",
              "sysVersion": "1"
            }
          ]
        },
        "quantity": {
          "value": "50",
          "units": "cm",
          "code": "1",
          "description": "centi meter",
          "sysId": "1",
          "sysName": "UOM code",
          "sysVersion": "UOM version"
        }
      },
      "specimenLength": "0.07",
      "specimenWidth": "0.05",
      "specimenHeight": "0.03",
      "sizeUnitOfMeasure": {
        "code": "1",
        "display": "cm",
        "description": "centi meter",
        "sysId": "1",
        "sysName": "UOM code",
        "sysVersion": "UOM version"
      },
      "mininumCutThickness": "0.00005",
      "maximumCutThickness": "0.00008",
      "cutThicknessUnitOfMeasure": {
        "code": "1",
        "display": "cm",
        "description": "centi meter",
        "sysId": "1",
        "sysName": "UOM code",
        "sysVersion": "UOM version"
      },
      "specimenInitialWeight": "1.008",
      "specimenIntermediateWeight": "1.003",
      "specimenFinalWeight": "1",
      "weightUnitOfMeasure": {
        "code": "1",
        "display": "cm",
        "description": "centi meter",
        "sysId": "1",
        "sysName": "UOM code",
        "sysVersion": "UOM version"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/subjects/1"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "/HSDataService-web/api/3.2.0/subjectapi/clinicalspecimens?id=1&id=2"
    }
  ]
}