REST API for Oracle Healthcare Translational Research

Retrieve Genomic Specimen Metadata for Specimen Identifier

get

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

This endpoints supports the retrieval of Genomic Specimen Metadata for a Specimen Identifier. It returns Genomic Specimen Metadata information like Category Name , Tag, String Value, Number Value, Date Value and other Genomic Specimen Metadata associated information.

Request

Supported Media Types

application/json
application/xml

Path Parameters

id: Type: integer (int64)

Required: true

Query Parameters

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

Root 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 request parameters

404 Response

Specimen metadata not found

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/48784/metadata

Example of Response Body

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

{
  "resourceType": "GenomicSpecimenMetadata",
  "items": [
    {
      "categoryName": "ANALYSIS",
      "metadata": [
        {
          "tag": "DATATYPE",
          "strValue": "variant"
        },
        {
          "tag": "GENOMEBUILD",
          "strValue": "GRCh37"
        },
        {
          "tag": "ANALYSISSYS",
          "strValue": "NGS"
        },
        {
          "tag": "DELETEEXISTINGRESULT",
          "strValue": "Y"
        },
        {
          "tag": "ANALYSISID",
          "strValue": "GENOME_GPS"
        },
        {
          "tag": "ANALYSISVERSION",
          "strValue": "2.0.2"
        },
        {
          "tag": "ANALYSISDATE",
          "strValue": "03/04/2015 02:43",
          "dateValue": "03/04/2015"
        },
        {
          "tag": "DATAFILE",
          "strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
        }
      ]
    },
    {
      "categoryName": "RUN",
      "metadata": [
        {
          "tag": "FLOWCELLID",
          "strValue": "UNKNOWN"
        },
        {
          "tag": "CAPTUREKIT",
          "strValue": "Agilent SS Custom Capture"
        },
        {
          "tag": "RUNID",
          "strValue": "145186"
        },
        {
          "tag": "READTYPE",
          "strValue": "Paired End Reads"
        },
        {
          "tag": "LANENUMBER",
          "strValue": "2",
          "numValue": 2
        },
        {
          "tag": "CYCLE",
          "strValue": "1014"
        },
        {
          "tag": "CUSTOMINDEX",
          "strValue": "IGCCAAT"
        },
        {
          "tag": "APPLICATIONTYPE",
          "strValue": "exome"
        },
        {
          "tag": "ISVENDORINDEX",
          "strValue": "UNKNOWN"
        }
      ]
    },
    {
      "categoryName": "SPECIMEN",
      "metadata": [
        {
          "tag": "ADDSAMPLEMETAFILE",
          "strValue": "Y"
        },
        {
          "tag": "ADDSAMPLEMETAFILE",
          "strValue": "Y"
        },
        {
          "tag": "SAMPLEIDSOURCE",
          "strValue": "MAYO_RLIMS"
        },
        {
          "tag": "SAMPLEIDSOURCE",
          "strValue": "MAYO_RLIMS"
        },
        {
          "tag": "REQUESTTU",
          "strValue": "tu0"
        },
        {
          "tag": "ISCLINICAL",
          "strValue": "N"
        },
        {
          "tag": "ISCLINICAL",
          "strValue": "N"
        },
        {
          "tag": "SPECIESNAME",
          "strValue": "Homo sapiens"
        },
        {
          "tag": "SPECIESNAME",
          "strValue": "Homo sapiens"
        },
        {
          "tag": "PROJECTID",
          "strValue": "NGSLBP-1407602"
        },
        {
          "tag": "IRB",
          "strValue": "14-001385"
        }
      ]
    }
  ],
  "count": 3,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7001/HSDataService-web/api/3.2.0/patientapi/genomicspecimens/48784/metadata"
    }
  ]
}