An example of a herd screening ELISA assay for Mycoplasmal Pneumonia in Pigs.

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

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

#   
# An example of a herd screening observation for Mycoplasmal Pneumonia in Pigs
#(Enzootic pneumonia).  Many thanks to Veterinary Diagnostic Laboratory Iowa State University for the data.
#This uses the Group resource as the subject 

[a fhir:Observation ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "herd1"] ; # 
  fhir:status [ fhir:v "final"] ; #    the mandatory status   
  fhir:category ( [
     fhir:coding ( [
       fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
       fhir:code [ fhir:v "laboratory" ] ;
       fhir:display [ fhir:v "Laboratory" ]
     ] ) ;
     fhir:text [ fhir:v "Laboratory" ]
  ] ) ; #   category code is A code that classifies the general type of observation being made. This is used for searching, sorting and display purposes. 
  fhir:code [
     fhir:coding ( [
       a loinc:80219-9 ;
       fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
       fhir:code [ fhir:v "80219-9" ] ;
       fhir:display [ fhir:v "Mycoplasma hyopneumoniae Ab sample/Positive control in Serum by Immunoassay" ] #  more generic methodless LOINC 
     ] [
       fhir:system [ fhir:v "http://acme.org/devices/clinical-codes"^^xsd:anyURI ] ;
       fhir:code [ fhir:v "Mycoplasma" ] ;
       fhir:display [ fhir:v "Mycoplasma" ]
     ] ) ; #    LOINC - always recommended to have a LOINC code   
     fhir:text [ fhir:v "Mycoplasma hyopneumoniae - MHP" ]
  ] ; #   
#    Observations are often coded in multiple code systems.
#      - LOINC provides codes of varying granularity (though not usefully more specific in this particular case) and more generic LOINCs  can be mapped to more specific codes as shown here
#      - snomed provides a clinically relevant code that is usually less granular than LOINC
#      - the source system provides its own code, which may be less or more granular than LOINC
#    
  fhir:subject [
     fhir:reference [ fhir:v "Group/herd1" ]
  ] ; #     subject is a herd of 2500 breding sows  
  fhir:encounter [
     fhir:display [ fhir:v "part of a health assurance program" ]
  ] ; # 
  fhir:effective [ fhir:v "2017-11-20"^^xsd:date] ; # 
  fhir:value [
     a fhir:Quantity ;
     fhir:value [ fhir:v "0.2"^^xsd:decimal ] ;
     fhir:unit [ fhir:v "% (sample/positive control)" ] ;
     fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ;
     fhir:code [ fhir:v "%" ]
  ] ; #    In FHIR, units may be represented twice. Once in the
#    agreed human representation, and once in a coded form.
#    Both is best, since it's not always possible to infer
#    one from the other in code.
#
#    When a computable unit is provided, UCUM (http://unitsofmeasure.org)
#    is always preferred, but it doesn't provide notional units (such as
#    "tablet"), etc. For these, something else is required (e.g. SNOMED CT)
#     
  fhir:interpretation ( [
     fhir:coding ( [
       fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"^^xsd:anyURI ] ;
       fhir:code [ fhir:v "NEG" ] ;
       fhir:display [ fhir:v "Negative" ]
     ] ) ;
     fhir:text [ fhir:v "Negative" ]
  ] ) ; # 
  fhir:specimen [
     fhir:reference [ fhir:v "Specimen/pooled-serum" ] ;
     fhir:display [ fhir:v "30 serum" ]
  ] ; #   Specimen is a pooled serology sample of 30 animals. 
  fhir:referenceRange ( [
     fhir:text [ fhir:v ">0.4 Positive; 0.3 to 0.4 Suspect < 0.3 Negative" ]
  ] )] . # 

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