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-omop | Version: 0.1.0-ci-build | |||
| Draft as of 2026-09-28 | Computable Name: DmMicrobiologyToOmop | |||
The OMOP concepts for each column of the DMv1.2 microbiology table, from the DM → FHIR → OMOP crosswalk. Each target's comment names the OMOP CDM field it fills. equivalent: the column's own concept; narrower: one of several concepts the column's values map to; relatedto: a value, unit or qualifier concept. Concept IDs of 2000000000 and above are PROTECT-CHILD custom concepts (CodeSystem ProtectChildOmopVocabulary).
This mapping does not specify any particular context of use.
Mapping from PROTECT-CHILD Data Model Variables to OHDSI Standardized Vocabularies
| Source Concept Details | Relationship | Target Concept Details | Comment | ||
| Codes from PROTECT-CHILD Data Model Variables | Codes from OHDSI Standardized Vocabularies | ||||
| microbiology.ebv_dna | microbiology.ebv_dna | is equivalent to | 3012570 | Epstein Barr virus DNA [Presence] in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.ebv_dna_copies | microbiology.ebv_dna_copies | is equivalent to | 3037329 | Epstein Barr virus DNA [#/volume] (viral load) in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 8799 | copies per milliliter | OMOP MEASUREMENT.unit_concept_id; vocabulary UCUM. | ||
| microbiology.ebv_igm_anti_ea | microbiology.ebv_igm_anti_ea | is equivalent to | 3033477 | Epstein Barr virus early Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.ebv_igm_anti_vca | microbiology.ebv_igm_anti_vca | is equivalent to | 3012732 | Epstein Barr virus nuclear IgM Ab [Presence] in Serum **(correction needed: this is EBNA IgM, LOINC 7884-0; the variable is VCA IgM, LOINC 30340-4)** | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.ebv_igg_anti_vca | microbiology.ebv_igg_anti_vca | is equivalent to | 3006585 | Epstein Barr virus capsid IgG Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.ebv_igg_ebna | microbiology.ebv_igg_ebna | is equivalent to | 3021849 | Epstein Barr virus nuclear IgG Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.cmv_dna | microbiology.cmv_dna | is equivalent to | 3021884 | Cytomegalovirus DNA [Presence] in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.cmv_dna_copies | microbiology.cmv_dna_copies | is equivalent to | 3024974 | Cytomegalovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 8799 | copies per milliliter | OMOP MEASUREMENT.unit_concept_id; vocabulary UCUM. | ||
| microbiology.cmv_igm | microbiology.cmv_igm | is equivalent to | 3013332 | Cytomegalovirus IgM Ab [Presence] in Serum or Plasma | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.cmv_igg | microbiology.cmv_igg | is equivalent to | 3012887 | Cytomegalovirus IgG Ab [Presence] in Serum or Plasma by Immunoassay | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.parvovirus_b19_dna | microbiology.parvovirus_b19_dna | is equivalent to | 3032435 | Parvovirus B19 DNA [Presence] in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.parvovirus_b19_dna_copies | microbiology.parvovirus_b19_dna_copies | is equivalent to | 3032993 | Parvovirus B19 DNA [#/volume] (viral load) in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 8799 | copies per milliliter | OMOP MEASUREMENT.unit_concept_id; vocabulary UCUM. | ||
| microbiology.parvovirus_b19_igg | microbiology.parvovirus_b19_igg | is equivalent to | 3006410 | Parvovirus B19 IgG Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.parvovirus_b19_igm | microbiology.parvovirus_b19_igm | is equivalent to | 3008321 | Parvovirus B19 IgM Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.hsv_igg | microbiology.hsv_igg | is equivalent to | 3020134 | Herpes simplex virus IgG Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45880296 | Not detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45877985 | Detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.hsv_igm | microbiology.hsv_igm | is equivalent to | 3010761 | Herpes simplex virus IgM Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.adenovirus_igg | microbiology.adenovirus_igg | is equivalent to | 3040947 | Adenovirus IgG Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.adenovirus_igm | microbiology.adenovirus_igm | is equivalent to | 3036242 | Adenovirus IgM Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.blood_adenovirus_dna | microbiology.blood_adenovirus_dna | is equivalent to | 36203755 | Adenovirus DNA [Presence] in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.blood_adenovirus_dna_copies | microbiology.blood_adenovirus_dna_copies | is equivalent to | 3028979 | Adenovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 8799 | copies per milliliter | OMOP MEASUREMENT.unit_concept_id; vocabulary UCUM. | ||
| microbiology.vzv_igg | microbiology.vzv_igg | is equivalent to | 3022386 | Varicella zoster virus IgG Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.vzv_igm | microbiology.vzv_igm | is equivalent to | 3016065 | Varicella zoster virus IgM Ab [Presence] in Serum | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.blood_bkv_dna | microbiology.blood_bkv_dna | is equivalent to | 40766205 | BK virus DNA [Presence] in Blood | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45878583 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45884084 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.blood_bkv_dna_copies | microbiology.blood_bkv_dna_copies | is equivalent to | 3029226 | BK virus DNA [#/volume] (viral load) in Blood by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 8799 | copies per milliliter | OMOP MEASUREMENT.unit_concept_id; vocabulary UCUM. | ||
| microbiology.urine_bkv_dna | microbiology.urine_bkv_dna | is equivalent to | 3029173 | BK virus DNA [Presence] in Urine by NAA with probe detection | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45880296 | Not detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45877985 | Detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.bkv_dna_kidney_biopsy | microbiology.bkv_dna_kidney_biopsy | is equivalent to | 1091792 | BK virus DNA [Presence] in Specimen | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45880296 | Not detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45877985 | Detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| microbiology.bkv_fish_kidney_biopsy | microbiology.bkv_fish_kidney_biopsy | is equivalent to | 1091792 | BK virus DNA [Presence] in Specimen | OMOP MEASUREMENT.measurement_concept_id; vocabulary LOINC. |
| is related to | 45880296 | Not detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is related to | 45877985 | Detected | OMOP MEASUREMENT.value_as_concept_id; vocabulary LOINC. | ||
| is equivalent to | 1073315 | Fluorescence in situ hybridization technique | OMOP OBSERVATION.observation_concept_id; vocabulary SNOMED. | ||
| microbiology.blood_colture | microbiology.blood_colture | is equivalent to | 4107893 | Blood culture | OMOP MEASUREMENT.measurement_concept_id; vocabulary SNOMED. |
| is related to | 9189 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary SNOMED. | ||
| is related to | 9191 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary SNOMED. | ||
| microbiology.urine_colture | microbiology.urine_colture | is equivalent to | 4024509 | Urine culture | OMOP MEASUREMENT.measurement_concept_id; vocabulary SNOMED. |
| is related to | 9189 | Negative | OMOP MEASUREMENT.value_as_concept_id; vocabulary SNOMED. | ||
| is related to | 9191 | Positive | OMOP MEASUREMENT.value_as_concept_id; vocabulary SNOMED. | ||
| microbiology.ebv_hepatitis_liver | microbiology.ebv_hepatitis_liver | is equivalent to | 4119142 | Epstein-Barr virus hepatitis | OMOP CONDITION_OCCURRENCE.condition_concept_id; vocabulary SNOMED. |
| microbiology.evidence_bkvan | microbiology.evidence_bkvan | is equivalent to | 37017585 | BK virus nephropathy | OMOP CONDITION_OCCURRENCE.condition_concept_id; vocabulary SNOMED. |