Bacterial Isolate from Stool sample

@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 "isolate"]; # 
  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=\"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 \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/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 \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/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>
    <status value="generated" />
    <div xmlns="http://www.w3.org/1999/xhtml">[Put rendering here]</div>
  </text>  
  fhir:DomainResource.contained [
     a fhir:Specimen;
     fhir:index 0;
     fhir:Resource.id [ fhir:value "stool" ];
     fhir:Specimen.accessionIdentifier [
       fhir:Identifier.system [ fhir:value "http://lab.acme.org/specimens/2015" ]; #    accession identifier - e.g. assigned by the labaratory when it is received.\n     This is common, unlike specimen identifier   
       fhir:Identifier.value [ fhir:value "X352356" ]
     ];
     fhir:Specimen.status [ fhir:value "unavailable" ];
     fhir:Specimen.type [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:119339001;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "119339001" ];
         fhir:Coding.display [ fhir:value "Stool 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 \n  
     ];
     fhir:Specimen.subject [
       fhir:Reference.reference [ fhir:value "Patient/example" ]
     ];
     fhir:Specimen.receivedTime [ fhir:value "2015-08-16T07:03:00Z"^^xsd:dateTime ];
     fhir:Specimen.collection [
       fhir:Specimen.collection.collector [
         fhir:Reference.display [ fhir:value "Patient" ] #      in practice, collecter is almost always recorded     
       ];
       fhir:Specimen.collection.collectedDateTime [ fhir:value "2011-08-16T06:15:00Z"^^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.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.accessionIdentifier [
     fhir:Identifier.system [ fhir:value "http://lab.acme.org/specimens/2011" ];
     fhir:Identifier.value [ fhir:value "X352356-ISO1" ]
  ]; # 
  fhir:Specimen.status [ fhir:value "available"]; # 
  fhir:Specimen.type [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a sct:429951000124103;
       fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
       fhir:Coding.code [ fhir:value "429951000124103" ];
       fhir:Coding.display [ fhir:value "Bacterial isolate specimen" ]
     ]
  ]; # 
  fhir:Specimen.subject [
     fhir:Reference.reference [ fhir:value "Patient/example" ]
  ]; # 
  fhir:Specimen.receivedTime [ fhir:value "2015-08-18T07:03:00Z"^^xsd:dateTime]; # 
  fhir:Specimen.parent [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "#stool" ]
  ]; # 
  fhir:Specimen.role [
     fhir:index 0;
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.code [ fhir:value "p" ];
       fhir:Coding.display [ fhir:value "Patient" ]
     ]
  ]; # 
  fhir:Specimen.collection [
     fhir:Specimen.collection.collector [
       fhir:Reference.reference [ fhir:value "Practitioner/f202" ] #      in practice, collecter is almost always recorded     
     ];
     fhir:Specimen.collection.collectedDateTime [ fhir:value "2015-08-16T07:03:00Z"^^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.method [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0488" ];
         fhir:Coding.code [ fhir:value "BAP" ]
       ]
     ] #      method is usually implied by type     
  ]; # 
  fhir:Specimen.note [
     fhir:index 0;
     fhir:Annotation.text [ fhir:value "Patient dropped off specimen" ]
  ]] . # 

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

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

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