REST API for Oracle Healthcare Translational Research

Retrieve Genomic Specimen details for Clinical Specimen Identifiers

get

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

This endpoint supports the retrieval of Genomic Specimens for multiple Clinical Specimen Identifiers 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: Type: string

Required: true

Pattern: patientapi|subjectapi

Query Parameters

id

Type: array

Collection Format: multi

Zero or more Clinical Specimen Row IDs

Items

Type: integer (int64)

limit

Type: integer (int32)

Number of rows to return

offset

Type: integer (int32)

Row number to start from

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Model for paginated collections of data.

Root Schema : PageableCollectionGenomicSpecimen

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 GenomicSpecimen

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 : GenomicSpecimen

Type: object

Properties

genomicFileMetadata: Type: object LinkedReference
genomicSpecimenMetadata: Type: object LinkedReference
identifier: Type: object Identifier

Identifier assigned by a given system
patient: Type: object LinkedReference
resourceType: Type: string
specimenNumber: Type: string

Specimen identifier in linked Specimen Datasource Database
specimenVendorNumber: Type: string

Vendor Identifier in linked Specimen Datasource Database
subject: Type: object LinkedReference

Nested Schema : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

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

400 Response

Invalid parameters supplied

404 Response

Specimen(s) not found

Examples

The following example submits a GET request.

API URL — Patient Context

http://localhost:7001/HSDataService-web/api/3.2.0/patientapi/genomicspecimens?id=62891&id=62892&id=62893&id=62894&id=62895&id=62896&limit=10&offset=0

Example of Response Body

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

{
  "resourceType": "GenomicSpecimen",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "49453"
      },
      "specimenNumber": "HG00154",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49453/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49453/fileMetadata"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/patients/498638"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49454"
      },
      "specimenNumber": "HG00155",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49454/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49454/fileMetadata"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/patients/498639"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49455"
      },
      "specimenNumber": "HG00157",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49455/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49455/fileMetadata"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/patients/498640"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49456"
      },
      "specimenNumber": "HG00158",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49456/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49456/fileMetadata"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/patients/498641"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49457"
      },
      "specimenNumber": "HG00159",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49457/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49457/fileMetadata"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/patients/498642"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49458"
      },
      "specimenNumber": "HG00160",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49458/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/49458/fileMetadata"
      },
      "patient": {
        "reference": "/HSDataService-web/api/3.2.0/patientapi/patients/498643"
      }
    }
  ],
  "count": 6,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/patientapi/genomicspecimens?id=62891&id=62892&id=62893&id=62894&id=62895&id=62896&limit=10&offset=0"
    }
  ]
}

API URL — Subject Context

http://localhost:7001/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens?id=1&id=2&id=3&id=4&limit=10&offset=0

Example of Response Body

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

{
  "resourceType": "GenomicSpecimen",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "40001"
      },
      "specimenNumber": "ADME_SPEC1",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40001/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40001/fileMetadata"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/subjects/7"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "40002"
      },
      "specimenNumber": "ADME_SPEC10",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40002/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40002/fileMetadata"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/subjects/8"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "40003"
      },
      "specimenNumber": "ADME_SPEC100",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40003/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40003/fileMetadata"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/subjects/9"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "40004"
      },
      "specimenNumber": "ADME_SPEC1000",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40004/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens/40004/fileMetadata"
      },
      "subject": {
        "reference": "/HSDataService-web/api/3.2.0/subjectapi/subjects/10"
      }
    }
  ],
  "count": 4,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/subjectapi/genomicspecimens?id=1&id=2&id=3&id=4&limit=10&offset=0"
    }
  ]
}