Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genomic Specimen details for Clinical Specimen Identifiers

get

/ohfapi/cg/v3.3/{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: string

Pattern: patientapi|subjectapi

Query Parameters

id(optional): array

Collection Format: multi

Zero or more Clinical Specimen Row IDs

[0]: integer(int64)

{
    "name":"id",
    "in":"query",
    "description":"Zero or more Clinical Specimen Row IDs",
    "required":false,
    "type":"array",
    "items":{
        "type":"integer",
        "format":"int64"
    },
    "collectionFormat":"multi"
}

limit(optional): integer(int32)

Number of rows to return
offset(optional): integer(int32)

Row number to start from

Security

basicAuth: basic

Type: basic

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

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

A boolean indicating if more pages are available.
items(optional): array items

A collection of paged items.
links(optional): array links

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":{
                "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."
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "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":{
        "wrapped":true
    },
    "description":"A collection of paged items.",
    "items":{
        "$ref":"#/definitions/GenomicSpecimen"
    }
}

Nested Schema : links

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":{
        "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

Specimen(s) not found

Examples

The following example submits a GET request.

API URL ??? Patient Context

http://localhost:7010/ohfapi/cg/v3.3/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": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49453/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49453/fileMetadata"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/patients/498638"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49454"
      },
      "specimenNumber": "HG00155",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49454/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49454/fileMetadata"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/patients/498639"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49455"
      },
      "specimenNumber": "HG00157",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49455/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49455/fileMetadata"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/patients/498640"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49456"
      },
      "specimenNumber": "HG00158",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49456/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49456/fileMetadata"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/patients/498641"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49457"
      },
      "specimenNumber": "HG00159",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49457/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49457/fileMetadata"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/patients/498642"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "49458"
      },
      "specimenNumber": "HG00160",
      "specimenVendorNumber": "vcf_wgs",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49458/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/patientapi/genomicspecimens/49458/fileMetadata"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/patients/498643"
      }
    }
  ],
  "count": 6,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/patientapi/genomicspecimens?id=62891&id=62892&id=62893&id=62894&id=62895&id=62896&limit=10&offset=0"
    }
  ]
}

API URL ??? Subject Context

http://localhost:7010/ohfapi/cg/v3.3/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": "/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"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "40002"
      },
      "specimenNumber": "ADME_SPEC10",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40002/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40002/fileMetadata"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/subjects/8"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "40003"
      },
      "specimenNumber": "ADME_SPEC100",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40003/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40003/fileMetadata"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/subjects/9"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "40004"
      },
      "specimenNumber": "ADME_SPEC1000",
      "specimenVendorNumber": "adme",
      "genomicSpecimenMetadata": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40004/metadata"
      },
      "genomicFileMetadata": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/genomicspecimens/40004/fileMetadata"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/subjects/10"
      }
    }
  ],
  "count": 4,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/subjectapi/genomicspecimens?id=1&id=2&id=3&id=4&limit=10&offset=0"
    }
  ]
}