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Example Specimen/isolate (XML)

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

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

Jump past Narrative

Bacterial Isolate from Stool sample (id = "isolate")

<?xml version="1.0" encoding="UTF-8"?>

<Specimen xmlns="http://hl7.org/fhir">
  <id value="isolate"/> 
    <!--   text>
    <status value="generated" />
    <div xmlns="http://www.w3.org/1999/xhtml">[Put rendering here]</div>
  </text>   -->

  <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative: Specimen</b> <a name="isolate"> </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> : id: 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> #429951000124103)</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="stool"> </a> </p> <blockquote> <p/>  <p> <a name="stool"> </a> </p> <p> <b> accessionIdentifier</b> : id: 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> -</td> <td> <b> Collector</b> </td> <td> <b> Collected[x]</b> </td> <td> <b> Method</b> </td> </tr> <tr> <td> *</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 
      (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/4.0.0/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> -</td> <td> <b> Collector</b> </td> <td> <b> Collected[x]</b> </td> <td> <b> Method</b> </td> </tr> <tr> <td> *</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 
      (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/4.0.0/CodeSystem-v2-0488.html">specimenCollectionMethod</a> #BAP)</span> </span> </td> </tr> </table> <p> <b> note</b> : Patient dropped off specimen</p> </div> </text> <contained> 
    <Specimen> 
      <id value="stool"/> 
      <accessionIdentifier> 
        <!--    accession identifier - e.g. assigned by the labaratory when it is received.
     This is common, unlike specimen identifier    -->
        <system value="http://lab.acme.org/specimens/2015"/> 
        <value value="X352356"/> 
      </accessionIdentifier> 
      <status value="unavailable"/> 
      <type> 
        <!--   
   Type is a loosely defined field because there is such a lot of variation in
         how it is used.
   The principal variation is how much information that could be represented elsewhere
         is also
   represented here. For instance, here's some possible types:
     lithium heparin plasma   (+ .container.additive) (e.g. SNOMED CT 446272009)
     transfusion bag of blood (+ container.type)
     Peritoneal lavage        (+ collection.bodySite)
   If the type includes other fields, it would be normal not to populate the other
         fields

   Note that this practice is so widespread that it's pointless to try and stop
         it 
   -->
        <coding> 
          <system value="http://snomed.info/sct"/> 
          <code value="119339001"/> 
          <display value="Stool specimen"/> 
        </coding> 
      </type> 
      <subject> 
        <reference value="Patient/example"/> 
      </subject> 
      <receivedTime value="2015-08-16T07:03:00Z"/> 
      <collection> 
        <collector> 
          <!--      in practice, collecter is almost always recorded      -->
          <display value="Patient"/> 
        </collector> 
        <!--      the time of collection is usually required. Usually a point in time, but can
         be a period 
      (collectedPeriod) if it's a timed collection (e.g. a 24 hour urine)      -->
        <collectedDateTime value="2011-08-16T06:15:00Z"/> 
        <!--      method is usually implied by type      -->
        <method> 
          <coding> 
            <system value="http://terminology.hl7.org/CodeSystem/v2-0488"/> 
            <code value="LNV"/> 
          </coding> 
        </method> 
      </collection> 
    </Specimen> 
  </contained> 
  <accessionIdentifier> 
    <system value="http://lab.acme.org/specimens/2011"/> 
    <value value="X352356-ISO1"/> 
  </accessionIdentifier> 
  <status value="available"/> 
  <type> 
    <coding> 
      <system value="http://snomed.info/sct"/> 
      <code value="429951000124103"/> 
      <display value="Bacterial isolate specimen"/> 
    </coding> 
  </type> 
  <subject> 
    <reference value="Patient/example"/> 
  </subject> 
  <receivedTime value="2015-08-18T07:03:00Z"/> 
  <parent> 
    <reference value="#stool"/> 
  </parent> 
  <role> 
    <coding> 
            <code value="p"/> 
      <display value="Patient"/> 
    </coding> 
  </role> 
  <collection> 
    <collector> 
      <!--      in practice, collecter is almost always recorded      -->
      <reference value="Practitioner/f202"/> 
    </collector> 
    <!--      the time of collection is usually required. Usually a point in time, but can
     be a period 
      (collectedPeriod) if it's a timed collection (e.g. a 24 hour urine)      -->
    <collectedDateTime value="2015-08-16T07:03:00Z"/> 
    <!--      method is usually implied by type      -->
    <method> 
      <coding> 
        <system value="http://terminology.hl7.org/CodeSystem/v2-0488"/> 
        <code value="BAP"/> 
      </coding> 
    </method> 
  </collection> 
  <note> 
    <text value="Patient dropped off specimen"/> 
  </note> 
</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.