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Example Specimen/isolate (Turtle)

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

Raw Turtle (+ also see Turtle/RDF Format Specification)

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>"
  ];
  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" ];
       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" ]
       ]
     ];
     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" ]
       ];
       fhir:Specimen.collection.collectedDateTime [ fhir:value "2011-08-16T06:15:00Z"^^xsd:dateTime ];
       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" ]
         ]
       ]
     ]
  ];
  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" ]
     ];
     fhir:Specimen.collection.collectedDateTime [ fhir:value "2015-08-16T07:03:00Z"^^xsd:dateTime ];
     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" ]
       ]
     ]
  ];
  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] .

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


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.