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Example Specimen/isolate (JSON)

Orders and Observations Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Device, Patient, Practitioner

Raw JSON (canonical form + also see JSON Format Specification)

Bacterial Isolate from Stool sample

{
  "resourceType" : "Specimen",
  "id" : "isolate",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Specimen</b><a name=\"isolate\"> </a><a name=\"hcisolate\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Specimen &quot;isolate&quot; </p></div><p><b>accessionIdentifier</b>: <code>http://lab.acme.org/specimens/2011</code>/X352356-ISO1</p><p><b>status</b>: available</p><p><b>type</b>: Bacterial isolate specimen <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#119303007 &quot;Microbial isolate specimen&quot;)</span></p><p><b>subject</b>: <a href=\"patient-example.html\">Patient/example</a> &quot;Peter CHALMERS&quot;</p><p><b>receivedTime</b>: 2015-08-18T07:03:00Z</p><p><b>parent</b>: <a name=\"hcstool\"> </a></p><blockquote><p/><p><a name=\"stool\"> </a></p><p><a name=\"hcstool\"> </a></p><p><b>accessionIdentifier</b>: <code>http://lab.acme.org/specimens/2015</code>/X352356</p><p><b>status</b>: unavailable</p><p><b>type</b>: Stool specimen <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#119339001)</span></p><p><b>subject</b>: <a href=\"patient-example.html\">Patient/example</a> &quot;Peter CHALMERS&quot;</p><p><b>receivedTime</b>: 2015-08-16T07:03:00Z</p><h3>Collections</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Collector</b></td><td><b>Collected[x]</b></td><td><b>Method</b></td></tr><tr><td style=\"display: none\">*</td><td><span>: Patient</span></td><td><span title=\"    the time of collection is usually required. Usually a point in time, but can be a period \n      (collectedPeriod) if it's a timed collection (e.g. a 24 hour urine)    \">2011-08-16T06:15:00Z</span></td><td><span title=\"    method is usually implied by type    \">Line, Venous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.5.0/CodeSystem-v2-0488.html\">specimenCollectionMethod</a>#LNV)</span></span></td></tr></table></blockquote><p><b>role</b>: Patient <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ([not stated]#p)</span></p><h3>Collections</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Collector</b></td><td><b>Collected[x]</b></td><td><b>Method</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"practitioner-example-f202-lm.html\">Practitioner/f202</a> &quot;Luigi Maas&quot;</td><td><span title=\"    the time of collection is usually required. Usually a point in time, but can be a period \n      (collectedPeriod) if it's a timed collection (e.g. a 24 hour urine)    \">2015-08-16T07:03:00Z</span></td><td><span title=\"    method is usually implied by type    \">Plates, Blood Agar <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.5.0/CodeSystem-v2-0488.html\">specimenCollectionMethod</a>#BAP)</span></span></td></tr></table><p><b>note</b>: Patient dropped off specimen</p><hr/><blockquote><p><b>Generated Narrative: Specimen #stool</b><a name=\"stool\"> </a><a name=\"hcstool\"> </a></p><p><b>accessionIdentifier</b>: <code>http://lab.acme.org/specimens/2015</code>/X352356</p><p><b>status</b>: unavailable</p><p><b>type</b>: Stool specimen <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#119339001)</span></p><p><b>subject</b>: <a href=\"patient-example.html\">Patient/example</a> &quot;Peter CHALMERS&quot;</p><p><b>receivedTime</b>: 2015-08-16T07:03:00Z</p><h3>Collections</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Collector</b></td><td><b>Collected[x]</b></td><td><b>Method</b></td></tr><tr><td style=\"display: none\">*</td><td><span>: Patient</span></td><td><span title=\"    the time of collection is usually required. Usually a point in time, but can be a period \n      (collectedPeriod) if it's a timed collection (e.g. a 24 hour urine)    \">2011-08-16T06:15:00Z</span></td><td><span title=\"    method is usually implied by type    \">Line, Venous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.5.0/CodeSystem-v2-0488.html\">specimenCollectionMethod</a>#LNV)</span></span></td></tr></table></blockquote></div>"
  },
  "contained" : [{
    "resourceType" : "Specimen",
    "id" : "stool",
    "accessionIdentifier" : {
      "system" : "http://lab.acme.org/specimens/2015",
      "value" : "X352356"
    },
    "status" : "unavailable",
    "type" : {
      "coding" : [{
        "system" : "http://snomed.info/sct",
        "code" : "119339001",
        "display" : "Stool specimen"
      }]
    },
    "subject" : {
      "reference" : "Patient/example"
    },
    "receivedTime" : "2015-08-16T07:03:00Z",
    "collection" : {
      "collector" : {
        "display" : "Patient"
      },
      "collectedDateTime" : "2011-08-16T06:15:00Z",
      "method" : {
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0488",
          "code" : "LNV"
        }]
      }
    }
  }],
  "accessionIdentifier" : {
    "system" : "http://lab.acme.org/specimens/2011",
    "value" : "X352356-ISO1"
  },
  "status" : "available",
  "type" : {
    "coding" : [{
      "system" : "http://snomed.info/sct",
      "code" : "119303007",
      "display" : "Microbial isolate specimen"
    }],
    "text" : "Bacterial isolate specimen"
  },
  "subject" : {
    "reference" : "Patient/example"
  },
  "receivedTime" : "2015-08-18T07:03:00Z",
  "parent" : [{
    "reference" : "#stool"
  }],
  "role" : [{
    "coding" : [{
      "code" : "p",
      "display" : "Patient"
    }]
  }],
  "collection" : {
    "collector" : {
      "reference" : "Practitioner/f202"
    },
    "collectedDateTime" : "2015-08-16T07:03:00Z",
    "method" : {
      "coding" : [{
        "system" : "http://terminology.hl7.org/CodeSystem/v2-0488",
        "code" : "BAP"
      }]
    }
  },
  "note" : [{
    "text" : "Patient dropped off specimen"
  }]
}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.