PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build -
PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build - ci-build
PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build - 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
| Official URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/ConceptMap/dm-microbiology-to-fhir | Version: 0.1.0-ci-build | |||
| Draft as of 2026-09-28 | Computable Name: DmMicrobiologyToFhir | |||
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.
Mapping from PROTECT-CHILD DM microbiology variables to (not specified)
Group 1 Mapping from PROTECT-CHILD Data Model Variables to Logical Observation Identifiers, Names and Codes (LOINC)
| Source Code | Relationship | Target Code | Comment |
| microbiology.ebv_dna | is equivalent to | 5002-1 (Epstein Barr virus DNA [Presence] in Blood by NAA with probe detection) | MicrobiologyNucleicAcid.code |
| microbiology.ebv_dna_copies | is equivalent to | 36923-1 (Epstein Barr virus DNA [#/volume] (viral load) in Blood by NAA with probe detection) | MicrobiologyViralLoad.code |
| microbiology.ebv_igm_anti_vca | is equivalent to | 30340-4 (Epstein Barr virus capsid IgM Ab [Presence] in Serum) | MicrobiologySerology.code. The OMOP sheet maps this to 3012732 (EBNA IgM, LOINC 7884-0), which is a different antigen. |
| microbiology.ebv_igg_anti_vca | is equivalent to | 30339-6 (Epstein Barr virus capsid IgG Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.ebv_igg_ebna | is equivalent to | 7883-2 (Epstein Barr virus nuclear IgG Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.cmv_dna | is equivalent to | 4996-5 (Cytomegalovirus DNA [Presence] in Blood by NAA with probe detection) | MicrobiologyNucleicAcid.code |
| microbiology.cmv_dna_copies | is equivalent to | 29604-6 (Cytomegalovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection) | MicrobiologyViralLoad.code |
| microbiology.cmv_igm | is equivalent to | 30325-5 (Cytomegalovirus IgM Ab [Presence] in Serum or Plasma) | MicrobiologySerology.code |
| microbiology.cmv_igg | is equivalent to | 13949-3 (Cytomegalovirus IgG Ab [Presence] in Serum or Plasma by Immunoassay) | MicrobiologySerology.code |
| microbiology.parvovirus_b19_dna | is equivalent to | 50348-2 (Parvovirus B19 DNA [Presence] in Blood by NAA with probe detection) | MicrobiologyNucleicAcid.code |
| microbiology.parvovirus_b19_dna_copies | is equivalent to | 49431-0 (Parvovirus B19 DNA [#/volume] (viral load) in Blood by NAA with probe detection) | MicrobiologyViralLoad.code |
| microbiology.parvovirus_b19_igg | is equivalent to | 29675-6 (Parvovirus B19 IgG Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.parvovirus_b19_igm | is equivalent to | 7981-4 (Parvovirus B19 IgM Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.hsv_igg | is equivalent to | 19106-4 (Herpes simplex virus IgG Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.hsv_igm | is equivalent to | 25435-9 (Herpes simplex virus IgM Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.adenovirus_igg | is equivalent to | 41162-9 (Adenovirus IgG Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.adenovirus_igm | is equivalent to | 21054-2 (Adenovirus IgM Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.blood_adenovirus_dna | is equivalent to | 86511-3 (Adenovirus DNA [Presence] in Blood by NAA with probe detection) | MicrobiologyNucleicAcid.code |
| microbiology.blood_adenovirus_dna_copies | is equivalent to | 49341-1 (Adenovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection) | MicrobiologyViralLoad.code |
| microbiology.vzv_igg | is equivalent to | 19162-7 (Varicella zoster virus IgG Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.vzv_igm | is equivalent to | 21597-0 (Varicella zoster virus IgM Ab [Presence] in Serum) | MicrobiologySerology.code |
| microbiology.blood_bkv_dna | is equivalent to | 63475-8 (BK virus DNA [Presence] in Blood) | MicrobiologyNucleicAcid.code |
| microbiology.blood_bkv_dna_copies | is equivalent to | 49345-2 (BK virus DNA [#/volume] (viral load) in Blood by NAA with probe detection) | MicrobiologyViralLoad.code |
| microbiology.urine_bkv_dna | is equivalent to | 33978-8 (BK virus DNA [Presence] in Urine by NAA with probe detection) | MicrobiologyNucleicAcid.code |
| microbiology.bkv_dna_kidney_biopsy | is equivalent to | 47251-4 (BK virus DNA [Presence] in Specimen by NAA with probe detection) | MicrobiologyNucleicAcid.code. Generic-specimen code; Observation.specimen identifies the kidney biopsy tissue. |
| microbiology.blood_colture | is equivalent to | 600-7 (Bacteria identified in Blood by Culture) | MicrobiologyCulture.code |
| microbiology.urine_colture | is equivalent to | 630-4 (Bacteria identified in Urine by Culture) | MicrobiologyCulture.code |
Group 2 Mapping from PROTECT-CHILD Data Model Variables to PROTECT-CHILD Microbiology Local Codes
| Source Code | Relationship | Target Code | Comment |
| microbiology.ebv_igm_anti_ea | is equivalent to | ebv-ea-igm (EBV early antigen IgM Ab [Presence] in Serum) | MicrobiologySerology.code. LOINC has no IgM-specific EBV early-antigen code; 7882-4 (early Ab, any isotype) is broader. |
| microbiology.bkv_fish_kidney_biopsy | is equivalent to | bkv-dna-ish-tissue (BK virus DNA [Presence] in Tissue by in situ hybridization) | MicrobiologyNucleicAcid.code. LOINC has no in-situ hybridisation code for BK virus in tissue. |
| microbiology.ebv_hepatitis_liver | is equivalent to | ebv-hepatitis-liver (EBV Hepatitis on liver) | MicrobiologyDiagnosis.code. MicrobiologyDiagnosis (Condition); false → the same Condition with verificationStatus #refuted; blank → no Condition. |
| microbiology.evidence_bkvan | is equivalent to | evidence-bkvan (Histological evidence of BKVAN) | MicrobiologyDiagnosis.code. MicrobiologyDiagnosis (Condition); No → the same Condition with verificationStatus #refuted; Unknown or blank → no Condition. |
Group 3 Mapping from PROTECT-CHILD Data Model Variables to unspecified code system
| Source Code | Relationship | Target Code | Comment |
| microbiology.other_positivity | (not mapped) | MicrobiologyReport.conclusion. DiagnosticReport.conclusion (free text, no code) | |