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Retrieve Genomic Specimen Metadata for Specimen Identifier

get

/ohfapi/cg/v3.3/{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: integer(int64)
  Minimum Value: 0

Query Parameters

• limit(optional): integer(int32)
  Number of rows to return
• offset(optional): integer(int32)
  Row number to start from

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root 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 request parameters

404 Response

Specimen metadata not found

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/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:7010/ohfapi/cg/v3.3/patientapi/genomicspecimens/48784/metadata"
    }
  ]
}

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