Microbiology component codes - TTL Representation - PROTECT-CHILD Pediatric Transplant Data Implementation Guide v0.1.0-ci-build

PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions
: Microbiology component codes - TTL Representation

Draft as of 2026-08-11
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@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 xsd: <http://www.w3.org/2001/XMLSchema#> .

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

<http://hl7.org/fhir/CodeSystem/microbiology-cs> a fhir:CodeSystem ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:Resource.id [ fhir:value "microbiology-cs"] ;
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ] ;
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem microbiology-cs</b></p><a name=\"microbiology-cs\"> </a><a name=\"hcmicrobiology-cs\"> </a><p>This case-insensitive code system <code>https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/microbiology-cs</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">microbiology-panel<a name=\"microbiology-cs-microbiology-panel\"> </a></td><td>Microbiology studies panel</td><td>Panel grouping microbiology and virology results for a visit.</td></tr><tr><td style=\"white-space:nowrap\">ebv-dna<a name=\"microbiology-cs-ebv-dna\"> </a></td><td>EBV-DNA (quantitative)</td><td>Epstein-Barr virus DNA detected/quantified by PCR.</td></tr><tr><td style=\"white-space:nowrap\">ebv-igm-anti-ea<a name=\"microbiology-cs-ebv-igm-anti-ea\"> </a></td><td>EBV IgM anti-EA</td><td>EBV IgM antibody to early antigen (EA).</td></tr><tr><td style=\"white-space:nowrap\">ebv-igm-anti-vca<a name=\"microbiology-cs-ebv-igm-anti-vca\"> </a></td><td>EBV IgM anti-VCA</td><td>EBV IgM antibody to viral capsid antigen (VCA).</td></tr><tr><td style=\"white-space:nowrap\">ebv-igg-anti-vca<a name=\"microbiology-cs-ebv-igg-anti-vca\"> </a></td><td>EBV IgG anti-VCA</td><td>EBV IgG antibody to viral capsid antigen (VCA).</td></tr><tr><td style=\"white-space:nowrap\">ebv-igg-ebna<a name=\"microbiology-cs-ebv-igg-ebna\"> </a></td><td>EBV IgG EBNA</td><td>EBV IgG antibody to Epstein-Barr nuclear antigen (EBNA).</td></tr><tr><td style=\"white-space:nowrap\">cmv-dna<a name=\"microbiology-cs-cmv-dna\"> </a></td><td>CMV-DNA</td><td>Cytomegalovirus DNA detected/quantified by PCR.</td></tr><tr><td style=\"white-space:nowrap\">cmv-igm<a name=\"microbiology-cs-cmv-igm\"> </a></td><td>CMV IgM</td><td>Cytomegalovirus IgM antibody.</td></tr><tr><td style=\"white-space:nowrap\">cmv-igg<a name=\"microbiology-cs-cmv-igg\"> </a></td><td>CMV IgG</td><td>Cytomegalovirus IgG antibody.</td></tr><tr><td style=\"white-space:nowrap\">parvovirus-b19-dna<a name=\"microbiology-cs-parvovirus-b19-dna\"> </a></td><td>Parvovirus B19 DNA</td><td>Parvovirus B19 DNA detected by PCR.</td></tr><tr><td style=\"white-space:nowrap\">parvovirus-b19-igg<a name=\"microbiology-cs-parvovirus-b19-igg\"> </a></td><td>Parvovirus B19 IgG</td><td>Parvovirus B19 IgG antibody.</td></tr><tr><td style=\"white-space:nowrap\">parvovirus-b19-igm<a name=\"microbiology-cs-parvovirus-b19-igm\"> </a></td><td>Parvovirus B19 IgM</td><td>Parvovirus B19 IgM antibody.</td></tr><tr><td style=\"white-space:nowrap\">hsv-igg<a name=\"microbiology-cs-hsv-igg\"> </a></td><td>HSV IgG</td><td>Herpes simplex virus IgG antibody.</td></tr><tr><td style=\"white-space:nowrap\">hsv-igm<a name=\"microbiology-cs-hsv-igm\"> </a></td><td>HSV IgM</td><td>Herpes simplex virus IgM antibody.</td></tr><tr><td style=\"white-space:nowrap\">adenovirus-igg<a name=\"microbiology-cs-adenovirus-igg\"> </a></td><td>Adenovirus IgG</td><td>Adenovirus IgG antibody.</td></tr><tr><td style=\"white-space:nowrap\">adenovirus-igm<a name=\"microbiology-cs-adenovirus-igm\"> </a></td><td>Adenovirus IgM</td><td>Adenovirus IgM antibody.</td></tr><tr><td style=\"white-space:nowrap\">vzv-igg<a name=\"microbiology-cs-vzv-igg\"> </a></td><td>VZV IgG</td><td>Varicella-zoster virus IgG antibody.</td></tr><tr><td style=\"white-space:nowrap\">vzv-igm<a name=\"microbiology-cs-vzv-igm\"> </a></td><td>VZV IgM</td><td>Varicella-zoster virus IgM antibody.</td></tr><tr><td style=\"white-space:nowrap\">blood-bkv-dna<a name=\"microbiology-cs-blood-bkv-dna\"> </a></td><td>Blood BKV-DNA</td><td>BK polyomavirus DNA in blood by PCR.</td></tr><tr><td style=\"white-space:nowrap\">urine-bkv-dna<a name=\"microbiology-cs-urine-bkv-dna\"> </a></td><td>Urine BKV-DNA</td><td>BK polyomavirus DNA in urine by PCR.</td></tr><tr><td style=\"white-space:nowrap\">bkv-dna-kidney-biopsy<a name=\"microbiology-cs-bkv-dna-kidney-biopsy\"> </a></td><td>BKV-DNA on kidney biopsy</td><td>BK polyomavirus DNA detected in kidney biopsy tissue.</td></tr><tr><td style=\"white-space:nowrap\">bkv-fish-kidney-biopsy<a name=\"microbiology-cs-bkv-fish-kidney-biopsy\"> </a></td><td>BKV FISH on kidney biopsy</td><td>BK polyomavirus detected by FISH in kidney biopsy tissue.</td></tr><tr><td style=\"white-space:nowrap\">ebv-dna-copies<a name=\"microbiology-cs-ebv-dna-copies\"> </a></td><td>EBV-DNA copies/ml</td><td>Quantitative EBV DNA viral load (copies/mL).</td></tr><tr><td style=\"white-space:nowrap\">cmv-dna-copies<a name=\"microbiology-cs-cmv-dna-copies\"> </a></td><td>CMV-DNA copies/ml</td><td>Quantitative CMV DNA viral load (copies/mL).</td></tr><tr><td style=\"white-space:nowrap\">parvovirus-b19-dna-copies<a name=\"microbiology-cs-parvovirus-b19-dna-copies\"> </a></td><td>Parvovirus B19 DNA copies/ml</td><td>Quantitative parvovirus B19 DNA viral load (copies/mL).</td></tr><tr><td style=\"white-space:nowrap\">blood-adenovirus-dna<a name=\"microbiology-cs-blood-adenovirus-dna\"> </a></td><td>Blood Adenovirus DNA</td><td>Adenovirus DNA in blood by PCR.</td></tr><tr><td style=\"white-space:nowrap\">blood-adenovirus-dna-copies<a name=\"microbiology-cs-blood-adenovirus-dna-copies\"> </a></td><td>Blood Adenovirus DNA copies/ml</td><td>Quantitative blood adenovirus DNA viral load (copies/mL).</td></tr><tr><td style=\"white-space:nowrap\">blood-bkv-dna-copies<a name=\"microbiology-cs-blood-bkv-dna-copies\"> </a></td><td>Blood BKV-DNA copies/ml</td><td>Quantitative blood BK virus DNA viral load (copies/mL).</td></tr><tr><td style=\"white-space:nowrap\">blood-colture<a name=\"microbiology-cs-blood-colture\"> </a></td><td>Blood culture</td><td>Blood culture for microbial growth.</td></tr><tr><td style=\"white-space:nowrap\">urine-colture<a name=\"microbiology-cs-urine-colture\"> </a></td><td>Urine culture</td><td>Urine culture for microbial growth.</td></tr><tr><td style=\"white-space:nowrap\">other-positivity<a name=\"microbiology-cs-other-positivity\"> </a></td><td>Other positivity</td><td>Other microbiological positivity not otherwise specified.</td></tr><tr><td style=\"white-space:nowrap\">ebv-hepatitis-liver<a name=\"microbiology-cs-ebv-hepatitis-liver\"> </a></td><td>EBV Hepatitis on liver</td><td>EBV-associated hepatitis involving the liver allograft.</td></tr><tr><td style=\"white-space:nowrap\">evidence-bkvan<a name=\"microbiology-cs-evidence-bkvan\"> </a></td><td>Histological evidence of BKVAN</td><td>Histological evidence of BK virus-associated nephropathy (BKVAN).</td></tr></table></div>"
  ] ;
  fhir:CodeSystem.url [ fhir:value "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/microbiology-cs"] ;
  fhir:CodeSystem.version [ fhir:value "0.1.0-ci-build"] ;
  fhir:CodeSystem.name [ fhir:value "MicrobiologyCS"] ;
  fhir:CodeSystem.title [ fhir:value "Microbiology component codes"] ;
  fhir:CodeSystem.status [ fhir:value "draft"] ;
  fhir:CodeSystem.experimental [ fhir:value "true"^^xsd:boolean] ;
  fhir:CodeSystem.date [ fhir:value "2026-08-11T12:50:29+00:00"^^xsd:dateTime] ;
  fhir:CodeSystem.publisher [ fhir:value "Protect Child"] ;
  fhir:CodeSystem.contact [
     fhir:index 0 ;
     fhir:ContactDetail.name [ fhir:value "Protect Child" ] ;
     fhir:ContactDetail.telecom [
       fhir:index 0 ;
       fhir:ContactPoint.system [ fhir:value "url" ] ;
       fhir:ContactPoint.value [ fhir:value "https://protect-child.eu/" ]
     ]
  ] ;
  fhir:CodeSystem.description [ fhir:value "Local codes for microbiology panel Observation components."] ;
  fhir:CodeSystem.caseSensitive [ fhir:value "false"^^xsd:boolean] ;
  fhir:CodeSystem.content [ fhir:value "complete"] ;
  fhir:CodeSystem.count [ fhir:value "33"^^xsd:nonNegativeInteger] ;
  fhir:CodeSystem.concept [
     fhir:index 0 ;
     fhir:CodeSystem.concept.code [ fhir:value "microbiology-panel" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Microbiology studies panel" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Panel grouping microbiology and virology results for a visit." ]
  ], [
     fhir:index 1 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV-DNA (quantitative)" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Epstein-Barr virus DNA detected/quantified by PCR." ]
  ], [
     fhir:index 2 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-igm-anti-ea" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV IgM anti-EA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "EBV IgM antibody to early antigen (EA)." ]
  ], [
     fhir:index 3 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-igm-anti-vca" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV IgM anti-VCA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "EBV IgM antibody to viral capsid antigen (VCA)." ]
  ], [
     fhir:index 4 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-igg-anti-vca" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV IgG anti-VCA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "EBV IgG antibody to viral capsid antigen (VCA)." ]
  ], [
     fhir:index 5 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-igg-ebna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV IgG EBNA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "EBV IgG antibody to Epstein-Barr nuclear antigen (EBNA)." ]
  ], [
     fhir:index 6 ;
     fhir:CodeSystem.concept.code [ fhir:value "cmv-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "CMV-DNA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Cytomegalovirus DNA detected/quantified by PCR." ]
  ], [
     fhir:index 7 ;
     fhir:CodeSystem.concept.code [ fhir:value "cmv-igm" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "CMV IgM" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Cytomegalovirus IgM antibody." ]
  ], [
     fhir:index 8 ;
     fhir:CodeSystem.concept.code [ fhir:value "cmv-igg" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "CMV IgG" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Cytomegalovirus IgG antibody." ]
  ], [
     fhir:index 9 ;
     fhir:CodeSystem.concept.code [ fhir:value "parvovirus-b19-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Parvovirus B19 DNA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Parvovirus B19 DNA detected by PCR." ]
  ], [
     fhir:index 10 ;
     fhir:CodeSystem.concept.code [ fhir:value "parvovirus-b19-igg" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Parvovirus B19 IgG" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Parvovirus B19 IgG antibody." ]
  ], [
     fhir:index 11 ;
     fhir:CodeSystem.concept.code [ fhir:value "parvovirus-b19-igm" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Parvovirus B19 IgM" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Parvovirus B19 IgM antibody." ]
  ], [
     fhir:index 12 ;
     fhir:CodeSystem.concept.code [ fhir:value "hsv-igg" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "HSV IgG" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Herpes simplex virus IgG antibody." ]
  ], [
     fhir:index 13 ;
     fhir:CodeSystem.concept.code [ fhir:value "hsv-igm" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "HSV IgM" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Herpes simplex virus IgM antibody." ]
  ], [
     fhir:index 14 ;
     fhir:CodeSystem.concept.code [ fhir:value "adenovirus-igg" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Adenovirus IgG" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Adenovirus IgG antibody." ]
  ], [
     fhir:index 15 ;
     fhir:CodeSystem.concept.code [ fhir:value "adenovirus-igm" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Adenovirus IgM" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Adenovirus IgM antibody." ]
  ], [
     fhir:index 16 ;
     fhir:CodeSystem.concept.code [ fhir:value "vzv-igg" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "VZV IgG" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Varicella-zoster virus IgG antibody." ]
  ], [
     fhir:index 17 ;
     fhir:CodeSystem.concept.code [ fhir:value "vzv-igm" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "VZV IgM" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Varicella-zoster virus IgM antibody." ]
  ], [
     fhir:index 18 ;
     fhir:CodeSystem.concept.code [ fhir:value "blood-bkv-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Blood BKV-DNA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "BK polyomavirus DNA in blood by PCR." ]
  ], [
     fhir:index 19 ;
     fhir:CodeSystem.concept.code [ fhir:value "urine-bkv-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Urine BKV-DNA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "BK polyomavirus DNA in urine by PCR." ]
  ], [
     fhir:index 20 ;
     fhir:CodeSystem.concept.code [ fhir:value "bkv-dna-kidney-biopsy" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "BKV-DNA on kidney biopsy" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "BK polyomavirus DNA detected in kidney biopsy tissue." ]
  ], [
     fhir:index 21 ;
     fhir:CodeSystem.concept.code [ fhir:value "bkv-fish-kidney-biopsy" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "BKV FISH on kidney biopsy" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "BK polyomavirus detected by FISH in kidney biopsy tissue." ]
  ], [
     fhir:index 22 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-dna-copies" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV-DNA copies/ml" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Quantitative EBV DNA viral load (copies/mL)." ]
  ], [
     fhir:index 23 ;
     fhir:CodeSystem.concept.code [ fhir:value "cmv-dna-copies" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "CMV-DNA copies/ml" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Quantitative CMV DNA viral load (copies/mL)." ]
  ], [
     fhir:index 24 ;
     fhir:CodeSystem.concept.code [ fhir:value "parvovirus-b19-dna-copies" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Parvovirus B19 DNA copies/ml" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Quantitative parvovirus B19 DNA viral load (copies/mL)." ]
  ], [
     fhir:index 25 ;
     fhir:CodeSystem.concept.code [ fhir:value "blood-adenovirus-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Blood Adenovirus DNA" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Adenovirus DNA in blood by PCR." ]
  ], [
     fhir:index 26 ;
     fhir:CodeSystem.concept.code [ fhir:value "blood-adenovirus-dna-copies" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Blood Adenovirus DNA copies/ml" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Quantitative blood adenovirus DNA viral load (copies/mL)." ]
  ], [
     fhir:index 27 ;
     fhir:CodeSystem.concept.code [ fhir:value "blood-bkv-dna-copies" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Blood BKV-DNA copies/ml" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Quantitative blood BK virus DNA viral load (copies/mL)." ]
  ], [
     fhir:index 28 ;
     fhir:CodeSystem.concept.code [ fhir:value "blood-colture" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Blood culture" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Blood culture for microbial growth." ]
  ], [
     fhir:index 29 ;
     fhir:CodeSystem.concept.code [ fhir:value "urine-colture" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Urine culture" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Urine culture for microbial growth." ]
  ], [
     fhir:index 30 ;
     fhir:CodeSystem.concept.code [ fhir:value "other-positivity" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Other positivity" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Other microbiological positivity not otherwise specified." ]
  ], [
     fhir:index 31 ;
     fhir:CodeSystem.concept.code [ fhir:value "ebv-hepatitis-liver" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "EBV Hepatitis on liver" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "EBV-associated hepatitis involving the liver allograft." ]
  ], [
     fhir:index 32 ;
     fhir:CodeSystem.concept.code [ fhir:value "evidence-bkvan" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Histological evidence of BKVAN" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Histological evidence of BK virus-associated nephropathy (BKVAN)." ]
  ] .

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

<http://hl7.org/fhir/CodeSystem/microbiology-cs.ttl> a owl:Ontology ;
  owl:imports fhir:fhir.ttl ;
  owl:versionIRI <http://build.fhir.org/CodeSystem/microbiology-cs.ttl> .