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Source1

{
  "resourceType": "ConceptMap",
  "id": "microbiology-lm-to-fhir",
  "text": {
    "status": "additional",
    "div": "<!-- snip (see above) -->"
  },
  "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/ConceptMap/microbiology-lm-to-fhir",
  "version": "0.1.0-ci-build",
  "name": "MicrobiologyLmToFhir",
  "title": "Microbiology logical model → FHIR",
  "status": "draft",
  "experimental": false,
  "date": "2026-09-28T06:51:47+00:00",
  "publisher": "Protect Child",
  "contact": [
    {
      "name": "Protect Child",
      "telecom": [
        {
          "system": "url",
          "value": "https://protect-child.eu/"
        }
      ]
    }
  ],
  "description": "Where each field of the Microbiology logical model lands in this guide's profiles. Generated from the model-map page; one group per target profile. Equivalence `relatedto` marks a field that is derived, split or recoded on the way.",
  "group": [
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/pcMicrobiologyLm",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-report",
      "element": [
        {
          "code": "pcMicrobiologyLm.microbiologyId",
          "display": "microbiology_id",
          "target": [
            {
              "code": "DiagnosticReport.identifier",
              "equivalence": "equivalent",
              "comment": "identifier"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.visitId",
          "display": "visit_id",
          "target": [
            {
              "code": "DiagnosticReport.encounter",
              "equivalence": "equivalent",
              "comment": "encounter. The recipient's Visit, also for donor results"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.donorId",
          "display": "donor_id",
          "target": [
            {
              "code": "DiagnosticReport.subject",
              "equivalence": "equivalent",
              "comment": "subject. Reference(Donor) for donor results; otherwise Reference(PatientTransplant)"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.otherPositivity",
          "display": "other_positivity",
          "target": [
            {
              "code": "DiagnosticReport.conclusion",
              "equivalence": "equivalent",
              "comment": "conclusion (free text) Kidney only"
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/pcMicrobiologyLm",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-nucleic-acid",
      "element": [
        {
          "code": "pcMicrobiologyLm.ebvDna",
          "display": "ebv_dna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 5002-1 — Epstein Barr virus DNA [Presence] in Blood by NAA with probe detection. Detected / Not detected"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.cmvDna",
          "display": "cmv_dna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 4996-5 — Cytomegalovirus DNA [Presence] in Blood by NAA with probe detection. Detected / Not detected"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.parvovirusB19Dna",
          "display": "parvovirus_b19_dna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 50348-2 — Parvovirus B19 DNA [Presence] in Blood by NAA with probe detection. Detected / Not detected. Alternatives: 75543-9"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.bloodAdenovirusDna",
          "display": "blood_adenovirus_dna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 86511-3 — Adenovirus DNA [Presence] in Blood by NAA with probe detection. Detected / Not detected"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.bloodBkvDna",
          "display": "blood_bkv_dna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 63475-8 — BK virus DNA [Presence] in Blood. Detected / Not detected"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.urineBkvDna",
          "display": "urine_bkv_dna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 33978-8 — BK virus DNA [Presence] in Urine by NAA with probe detection. Detected / Not detected"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.bkvDnaKidneyBiopsy",
          "display": "bkv_dna_kidney_biopsy",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 47251-4 — BK virus DNA [Presence] in Specimen by NAA with probe detection. Detected / Not detected. Generic-specimen code; Observation.specimen identifies the kidney biopsy tissue. Kidney only"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.bkvFishKidneyBiopsy",
          "display": "bkv_fish_kidney_biopsy",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "MicrobiologyCS#bkv-dna-ish-tissue — BK virus DNA [Presence] in Tissue by in situ hybridization. Detected / Not detected. LOINC has no in-situ hybridisation code for BK virus in tissue. Kidney only"
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/pcMicrobiologyLm",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-viral-load",
      "element": [
        {
          "code": "pcMicrobiologyLm.ebvDnaCopies",
          "display": "ebv_dna_copies",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 36923-1 — Epstein Barr virus DNA [#/volume] (viral load) in Blood by NAA with probe detection. Quantity. Alternatives: 93840-7, 47982-4, 43730-1"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.cmvDnaCopies",
          "display": "cmv_dna_copies",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 29604-6 — Cytomegalovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection. Quantity. Alternatives: 100675-8, 30247-1, 72493-0"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.parvovirusB19DnaCopies",
          "display": "parvovirus_b19_dna_copies",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 49431-0 — Parvovirus B19 DNA [#/volume] (viral load) in Blood by NAA with probe detection. Quantity. Alternatives: 49434-4, 74420-1"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.bloodAdenovirusDnaCopies",
          "display": "blood_adenovirus_dna_copies",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 49341-1 — Adenovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection. Quantity. Alternatives: 49334-6, 106727-1"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.bloodBkvDnaCopies",
          "display": "blood_bkv_dna_copies",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 49345-2 — BK virus DNA [#/volume] (viral load) in Blood by NAA with probe detection. Quantity. Alternatives: 101341-6, 41479-7, 32284-2"
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/pcMicrobiologyLm",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-serology",
      "element": [
        {
          "code": "pcMicrobiologyLm.ebvIgmAntiEa",
          "display": "ebv_igm_anti_ea",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "MicrobiologyCS#ebv-ea-igm — EBV early antigen IgM Ab [Presence] in Serum. Positive / Negative. LOINC has no IgM-specific EBV early-antigen code; 7882-4 (early Ab, any isotype) is broader."
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.ebvIgmAntiVca",
          "display": "ebv_igm_anti_vca",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 30340-4 — Epstein Barr virus capsid IgM Ab [Presence] in Serum. Positive / Negative. Alternatives: 24115-8, 40751-0, 93714-4; the OMOP sheet maps this to 3012732 (EBNA IgM, LOINC 7884-0), which is a different antigen."
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.ebvIggAntiVca",
          "display": "ebv_igg_anti_vca",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 30339-6 — Epstein Barr virus capsid IgG Ab [Presence] in Serum. Positive / Negative. Alternatives: 93713-6"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.ebvIggEbna",
          "display": "ebv_igg_ebna",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 7883-2 — Epstein Barr virus nuclear IgG Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.cmvIgm",
          "display": "cmv_igm",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 30325-5 — Cytomegalovirus IgM Ab [Presence] in Serum or Plasma. Positive / Negative. Alternatives: 87725-8"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.cmvIgg",
          "display": "cmv_igg",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 13949-3 — Cytomegalovirus IgG Ab [Presence] in Serum or Plasma by Immunoassay. Positive / Negative. Alternatives: 22244-8, 87726-6"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.parvovirusB19Igg",
          "display": "parvovirus_b19_igg",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 29675-6 — Parvovirus B19 IgG Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.parvovirusB19Igm",
          "display": "parvovirus_b19_igm",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 7981-4 — Parvovirus B19 IgM Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.hsvIgg",
          "display": "hsv_igg",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 19106-4 — Herpes simplex virus IgG Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.hsvIgm",
          "display": "hsv_igm",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 25435-9 — Herpes simplex virus IgM Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.adenovirusIgg",
          "display": "adenovirus_igg",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 41162-9 — Adenovirus IgG Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.adenovirusIgm",
          "display": "adenovirus_igm",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 21054-2 — Adenovirus IgM Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.vzvIgg",
          "display": "vzv_igg",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 19162-7 — Varicella zoster virus IgG Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.vzvIgm",
          "display": "vzv_igm",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 21597-0 — Varicella zoster virus IgM Ab [Presence] in Serum. Positive / Negative"
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/pcMicrobiologyLm",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-culture",
      "element": [
        {
          "code": "pcMicrobiologyLm.bloodColture",
          "display": "blood_colture",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 600-7 — Bacteria identified in Blood by Culture. Organism, or Positive / Negative. Kidney only"
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.urineColture",
          "display": "urine_colture",
          "target": [
            {
              "code": "Observation.value[x]",
              "equivalence": "equivalent",
              "comment": "LOINC 630-4 — Bacteria identified in Urine by Culture. Organism, or Positive / Negative. Kidney only"
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/pcMicrobiologyLm",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-diagnosis",
      "element": [
        {
          "code": "pcMicrobiologyLm.ebvHepatitisLiver",
          "display": "ebv_hepatitis_liver",
          "target": [
            {
              "code": "Condition.code",
              "equivalence": "relatedto",
              "comment": "SNOMED 302919001 Epstein-Barr virus hepatitis. presence = positive. Liver only. MicrobiologyDiagnosis (Condition). false → the same Condition with verificationStatus = #refuted; blank → no Condition."
            }
          ]
        },
        {
          "code": "pcMicrobiologyLm.evidenceBkvan",
          "display": "evidence_bkvan",
          "target": [
            {
              "code": "Condition.code",
              "equivalence": "relatedto",
              "comment": "SNOMED 713886006 BK virus nephropathy. presence = positive. MicrobiologyDiagnosis (Condition). No → the same Condition with verificationStatus = #refuted; Unknown or blank → no Condition."
            }
          ]
        }
      ]
    }
  ]
}