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Source1

{
  "resourceType": "ConceptMap",
  "id": "dm-microbiology-to-fhir",
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/ConceptMap/dm-microbiology-to-fhir",
  "version": "0.1.0-ci-build",
  "name": "DmMicrobiologyToFhir",
  "title": "DM microbiology columns → FHIR test codes",
  "status": "draft",
  "experimental": true,
  "date": "2026-09-28T06:51:47+00:00",
  "publisher": "Protect Child",
  "contact": [
    {
      "name": "Protect Child",
      "telecom": [
        {
          "system": "url",
          "value": "https://protect-child.eu/"
        }
      ]
    }
  ],
  "description": "Maps each column of the DMv1.2 microbiology table to the code of the Observation (or Condition) it becomes. Targets are the default codes; MicrobiologySerologyVS, MicrobiologyNucleicAcidVS and MicrobiologyViralLoadVS list accepted specimen-, method- and donor-specific alternatives. other_positivity has no code: it maps to MicrobiologyReport.conclusion.",
  "sourceCanonical": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/ValueSet/dm-microbiology-variable-vs",
  "group": [
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/dm-variable-cs",
      "target": "http://loinc.org",
      "element": [
        {
          "code": "microbiology.ebv_dna",
          "target": [
            {
              "code": "5002-1",
              "display": "Epstein Barr virus DNA [Presence] in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code"
            }
          ]
        },
        {
          "code": "microbiology.ebv_dna_copies",
          "target": [
            {
              "code": "36923-1",
              "display": "Epstein Barr virus DNA [#/volume] (viral load) in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyViralLoad.code"
            }
          ]
        },
        {
          "code": "microbiology.ebv_igm_anti_vca",
          "target": [
            {
              "code": "30340-4",
              "display": "Epstein Barr virus capsid IgM Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code. The OMOP sheet maps this to 3012732 (EBNA IgM, LOINC 7884-0), which is a different antigen."
            }
          ]
        },
        {
          "code": "microbiology.ebv_igg_anti_vca",
          "target": [
            {
              "code": "30339-6",
              "display": "Epstein Barr virus capsid IgG Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.ebv_igg_ebna",
          "target": [
            {
              "code": "7883-2",
              "display": "Epstein Barr virus nuclear IgG Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.cmv_dna",
          "target": [
            {
              "code": "4996-5",
              "display": "Cytomegalovirus DNA [Presence] in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code"
            }
          ]
        },
        {
          "code": "microbiology.cmv_dna_copies",
          "target": [
            {
              "code": "29604-6",
              "display": "Cytomegalovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyViralLoad.code"
            }
          ]
        },
        {
          "code": "microbiology.cmv_igm",
          "target": [
            {
              "code": "30325-5",
              "display": "Cytomegalovirus IgM Ab [Presence] in Serum or Plasma",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.cmv_igg",
          "target": [
            {
              "code": "13949-3",
              "display": "Cytomegalovirus IgG Ab [Presence] in Serum or Plasma by Immunoassay",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.parvovirus_b19_dna",
          "target": [
            {
              "code": "50348-2",
              "display": "Parvovirus B19 DNA [Presence] in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code"
            }
          ]
        },
        {
          "code": "microbiology.parvovirus_b19_dna_copies",
          "target": [
            {
              "code": "49431-0",
              "display": "Parvovirus B19 DNA [#/volume] (viral load) in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyViralLoad.code"
            }
          ]
        },
        {
          "code": "microbiology.parvovirus_b19_igg",
          "target": [
            {
              "code": "29675-6",
              "display": "Parvovirus B19 IgG Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.parvovirus_b19_igm",
          "target": [
            {
              "code": "7981-4",
              "display": "Parvovirus B19 IgM Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.hsv_igg",
          "target": [
            {
              "code": "19106-4",
              "display": "Herpes simplex virus IgG Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.hsv_igm",
          "target": [
            {
              "code": "25435-9",
              "display": "Herpes simplex virus IgM Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.adenovirus_igg",
          "target": [
            {
              "code": "41162-9",
              "display": "Adenovirus IgG Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.adenovirus_igm",
          "target": [
            {
              "code": "21054-2",
              "display": "Adenovirus IgM Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.blood_adenovirus_dna",
          "target": [
            {
              "code": "86511-3",
              "display": "Adenovirus DNA [Presence] in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code"
            }
          ]
        },
        {
          "code": "microbiology.blood_adenovirus_dna_copies",
          "target": [
            {
              "code": "49341-1",
              "display": "Adenovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyViralLoad.code"
            }
          ]
        },
        {
          "code": "microbiology.vzv_igg",
          "target": [
            {
              "code": "19162-7",
              "display": "Varicella zoster virus IgG Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.vzv_igm",
          "target": [
            {
              "code": "21597-0",
              "display": "Varicella zoster virus IgM Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code"
            }
          ]
        },
        {
          "code": "microbiology.blood_bkv_dna",
          "target": [
            {
              "code": "63475-8",
              "display": "BK virus DNA [Presence] in Blood",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code"
            }
          ]
        },
        {
          "code": "microbiology.blood_bkv_dna_copies",
          "target": [
            {
              "code": "49345-2",
              "display": "BK virus DNA [#/volume] (viral load) in Blood by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyViralLoad.code"
            }
          ]
        },
        {
          "code": "microbiology.urine_bkv_dna",
          "target": [
            {
              "code": "33978-8",
              "display": "BK virus DNA [Presence] in Urine by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code"
            }
          ]
        },
        {
          "code": "microbiology.bkv_dna_kidney_biopsy",
          "target": [
            {
              "code": "47251-4",
              "display": "BK virus DNA [Presence] in Specimen by NAA with probe detection",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code. Generic-specimen code; Observation.specimen identifies the kidney biopsy tissue."
            }
          ]
        },
        {
          "code": "microbiology.blood_colture",
          "target": [
            {
              "code": "600-7",
              "display": "Bacteria identified in Blood by Culture",
              "equivalence": "equivalent",
              "comment": "MicrobiologyCulture.code"
            }
          ]
        },
        {
          "code": "microbiology.urine_colture",
          "target": [
            {
              "code": "630-4",
              "display": "Bacteria identified in Urine by Culture",
              "equivalence": "equivalent",
              "comment": "MicrobiologyCulture.code"
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/dm-variable-cs",
      "target": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/microbiology-cs",
      "element": [
        {
          "code": "microbiology.ebv_igm_anti_ea",
          "target": [
            {
              "code": "ebv-ea-igm",
              "display": "EBV early antigen IgM Ab [Presence] in Serum",
              "equivalence": "equivalent",
              "comment": "MicrobiologySerology.code. LOINC has no IgM-specific EBV early-antigen code; 7882-4 (early Ab, any isotype) is broader."
            }
          ]
        },
        {
          "code": "microbiology.bkv_fish_kidney_biopsy",
          "target": [
            {
              "code": "bkv-dna-ish-tissue",
              "display": "BK virus DNA [Presence] in Tissue by in situ hybridization",
              "equivalence": "equivalent",
              "comment": "MicrobiologyNucleicAcid.code. LOINC has no in-situ hybridisation code for BK virus in tissue."
            }
          ]
        },
        {
          "code": "microbiology.ebv_hepatitis_liver",
          "target": [
            {
              "code": "ebv-hepatitis-liver",
              "display": "EBV Hepatitis on liver",
              "equivalence": "equivalent",
              "comment": "MicrobiologyDiagnosis.code. MicrobiologyDiagnosis (Condition); false → the same Condition with verificationStatus #refuted; blank → no Condition."
            }
          ]
        },
        {
          "code": "microbiology.evidence_bkvan",
          "target": [
            {
              "code": "evidence-bkvan",
              "display": "Histological evidence of BKVAN",
              "equivalence": "equivalent",
              "comment": "MicrobiologyDiagnosis.code. MicrobiologyDiagnosis (Condition); No → the same Condition with verificationStatus #refuted; Unknown or blank → no Condition."
            }
          ]
        }
      ]
    },
    {
      "source": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/dm-variable-cs",
      "element": [
        {
          "code": "microbiology.other_positivity",
          "target": [
            {
              "equivalence": "unmatched",
              "comment": "MicrobiologyReport.conclusion. DiagnosticReport.conclusion (free text, no code)"
            }
          ]
        }
      ]
    }
  ]
}