REST API for Oracle Healthcare Translational Research

Retrieve Clinical Specimens having Omics Data for Specimen Identifiers

get

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

This endpoint supports the retrieval of the Patient/Subject Clinical Specimens, which have at least one corresponding Omics Specimen, for the multiple Clinical Specimen Row IDs. It returns Paginated list of the Patient/Subject Clinical Specimens information like Identifier and Reference Link to the Patient/Subject details. If none of submitted Specimens has Omics Data, API returns 'Not Found' exception.

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

Required: true

Collection Format: multi

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

Patient/Subject Clinical Specimen Row IDs List

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

Clinical specimen or clinical specimen metadata not found

Examples

The following example submits a GET request.

API URL — Patient Context

http://localhost:7001/HSDataService-web/api/3.2.0/patientapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "Specimen",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "96"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/clinicalspecimens/96"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "97"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/clinicalspecimens/97"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/patientapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0"
    }
  ]
}

API URL — Subject Context

http://localhost:7001/HSDataService-web/api/3.2.0/subjectapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "Specimen",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "96"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/clinicalspecimens/96"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "97"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/clinicalspecimens/97"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/subjectapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0"
    }
  ]
}