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" ]
] )] . #
# -------------------------------------------------------------------------------------
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.