General Specimen Example

@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

[a fhir:Specimen;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "101"]; # 
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Specimen</b><a name=\"101\"> </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;101&quot; </p></div><p><b>identifier</b>: <span title=\" text&gt;\n    &lt;status value=&quot;generated&quot; /&gt;\n    &lt;div xmlns=&quot;http://www.w3.org/1999/xhtml&quot;&gt;[Put rendering here]&lt;/div&gt;\n  &lt;/text&gt; \">id: 23234352356</span></p><p><b>accessionIdentifier</b>: id: X352356</p><p><b>status</b>: available</p><p><b>type</b>: Venous blood specimen <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#122555007)</span></p><p><b>subject</b>: <a href=\"patient-example.html\">Patient/example: Peter Patient</a> &quot;Peter CHALMERS&quot;</p><p><b>receivedTime</b>: 2011-03-04T07:03:00Z</p><p><b>request</b>: <a href=\"servicerequest-example.html\">ServiceRequest/example</a></p><blockquote><p><b>collection</b></p><p><b>collector</b>: <a href=\"practitioner-example.html\">Practitioner/example</a> &quot;Adam CAREFUL&quot;</p><p><b>collected</b>: <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)  \">2011-05-30T06:15:00Z</span></p><p><b>quantity</b>: 6 mL</p><p><b>method</b>: <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></p><h3>BodySites</h3><table class=\"grid\"><tr><td>-</td><td><b>Concept</b></td></tr><tr><td>*</td><td>Structure of median cubital vein (body structure) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#49852007)</span></td></tr></table></blockquote><h3>Containers</h3><table class=\"grid\"><tr><td>-</td><td><b>Device</b></td><td><b>SpecimenQuantity</b></td></tr><tr><td>*</td><td><a href=\"broken-link.html\">Specimen/specimen-device-container-example-green-gel-vacutainer</a></td><td><span title=\"  if there's only one container, then this value is the same\n     as .collection.quantity (usually). This is for when there is more\n     than one container  \">3 mL</span></td></tr></table><p><b>note</b>: Specimen is grossly lipemic</p></div>"
  ]; #   text>
    <status value="generated" />
    <div xmlns="http://www.w3.org/1999/xhtml">[Put rendering here]</div>
  </text>  
  fhir:Specimen.identifier [
     fhir:index 0;
     fhir:Identifier.system [ fhir:value "http://ehr.acme.org/identifiers/collections" ]; #    a specimen identifier - e.g. assigned when the specimen was taken this is often not done   
     fhir:Identifier.value [ fhir:value "23234352356" ]
  ]; # 
  fhir:Specimen.accessionIdentifier [
     fhir:Identifier.system [ fhir:value "http://lab.acme.org/specimens/2011" ];
     fhir:Identifier.value [ fhir:value "X352356" ]
  ]; # 
  fhir:Specimen.status [ fhir:value "available"]; # 
  fhir:Specimen.type [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a sct:122555007;
       fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
       fhir:Coding.code [ fhir:value "122555007" ];
       fhir:Coding.display [ fhir:value "Venous blood specimen" ]
     ] #   \n   Type is a loosely defined field because there is such a lot of variation in how it is used.\n   The principal variation is how much information that could be represented elsewhere is also\n   represented here. For instance, here's some possible types:\n     lithium heparin plasma   (+ .container.additive) (e.g. SNOMED CT 446272009)\n     transfusion bag of blood (+ container.type)\n     Peritoneal lavage        (+ collection.bodySite)\n   If the type includes other fields, it would be normal not to populate the other fields\n\n   Note that this practice is so widespread that it's pointless to try and stop it   
  ]; # 
  fhir:Specimen.subject [
     fhir:Reference.reference [ fhir:value "Patient/example" ];
     fhir:Reference.display [ fhir:value "Peter Patient" ]
  ]; # 
  fhir:Specimen.receivedTime [ fhir:value "2011-03-04T07:03:00Z"^^xsd:dateTime]; # 
  fhir:Specimen.request [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "ServiceRequest/example" ] #    this points to the order that caused the sample to be drawn   
  ]; # 
  fhir:Specimen.collection [
     fhir:Specimen.collection.collector [
       fhir:Reference.reference [ fhir:value "Practitioner/example" ] #    in practice, collecter is almost always recorded   
     ];
     fhir:Specimen.collection.collectedDateTime [ fhir:value "2011-05-30T06:15:00Z"^^xsd:dateTime ]; #    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)   
     fhir:Specimen.collection.quantity [
       fhir:Quantity.value [ fhir:value "6"^^xsd:decimal ];
       fhir:Quantity.unit [ fhir:value "mL" ]
     ]; #    e.g. full   
     fhir:Specimen.collection.method [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0488" ];
         fhir:Coding.code [ fhir:value "LNV" ]
       ]
     ]; #    method is usually implied by type   
     fhir:Specimen.collection.bodySite [
       fhir:CodeableReference.concept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a sct:49852007;
           fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
           fhir:Coding.code [ fhir:value "49852007" ];
           fhir:Coding.display [ fhir:value "Structure of median cubital vein (body structure)" ]
         ]
       ]
     ] #    bodysite is usually implied by type too its here to demonstrate its usage to indicating the draw site in this case  
  ]; # 
  fhir:Specimen.container [
     fhir:index 0;
     fhir:Specimen.container.device [
       fhir:Reference.reference [ fhir:value "Specimen/specimen-device-container-example-green-gel-vacutainer" ]
     ];
     fhir:Specimen.container.specimenQuantity [
       fhir:Quantity.value [ fhir:value "3"^^xsd:decimal ];
       fhir:Quantity.unit [ fhir:value "mL" ]
     ] #    if there's only one container, then this value is the same\n     as .collection.quantity (usually). This is for when there is more\n     than one container   
  ]; #   
      the container identifier is not the same as the specimen identifier
      usually, it is pre-printed/implanted etc.on the container prior to
      use. It might a RFID in the container, or it might be a UDI
      (http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/UniqueDeviceIdentification/)
      
  fhir:Specimen.note [
     fhir:index 0;
     fhir:Annotation.text [ fhir:value "Specimen is grossly lipemic" ]
  ]] . # 

# - ontology header ------------------------------------------------------------

[a owl:Ontology;
  owl:imports fhir:fhir.ttl] .

# -------------------------------------------------------------------------------------