A study centre submitting paediatric kidney transplant records.

A study centre submitting paediatric liver transplant records.

Logical model for the PROTECT-CHILD bio_sample table.

Logical model for the PROTECT-CHILD clinical_event table. Each row captures either the start or the end of an episode. In FHIR the two rows for one episode fold into a single Condition, because two Conditions would make every completed episode count twice.

Logical model for the PROTECT-CHILD clinical_event_type table.

Logical model for the PROTECT-CHILD clinical_variable table. Includes weight, height, diuresis, and concomitant disease.

Logical model for the PROTECT-CHILD concomitant_medication table.

Logical model for the PROTECT-CHILD donor table.

Logical model for the PROTECT-CHILD imm_pat table. The phase maps to MedicationStatement.category; FHIR adds a rejection-treatment phase and a link from the treatment to the episode it was given for.

Logical model for the PROTECT-CHILD immunological_data table. Covers blood group, Rh, HLA allele typing, DSA, Banff category, C4d, and ANCA. In FHIR the row becomes an ImmunologicalDataReport grouping one Observation per result, plus a GraftBiopsy for the histopathology columns; see the Immunological Data map.

Logical model for the PROTECT-CHILD immunosuppressant catalogue table.

Logical model for the PROTECT-CHILD instrumental_investigation table.

Logical model for the PROTECT-CHILD lab_result table.

Logical model for the PROTECT-CHILD lab_test catalogue table.

Logical model for the PROTECT-CHILD microbiology table. Covers viral serology, DNA quantification, culture results, and BKVAN evidence.

Logical model for the PROTECT-CHILD patient table.

Logical model for the PROTECT-CHILD pre_medication table.

Logical model for the PROTECT-CHILD transplant table.

Logical model for the PROTECT-CHILD visit table. The FHIR side adds two things the table has no column for: a GraftEpisode anchored on the transplant date, so that 'before' and 'after' the transplant is a date comparison rather than a visit label, and a TransplantAdmission Encounter, so that the surgery and the post-operative period are not recorded inside a visit typed pre-transplant.

Logical model for the PROTECT-CHILD vital_sign table. Contains standard vitals and ABPM measurements.

Anti-neutrophil cytoplasmic antibody result (DMv1.2 immunological_data.anca). ANCA is an autoantibody test rather than a transplant-immunology finding; it stays with the immunological data because the DM records it on the immunological_data row. Recorded as Positive or Negative, so that a negative result is a result and not an absent Observation. Where the laboratory reports the pattern, use the c-ANCA (17353-4) or p-ANCA (17357-5) code, or the PR3 / MPO specificities.

One detected anti-HLA antibody, named by the HLA specificity it is directed against. One Observation per antibody: a patient commonly has several, each with its own specificity and strength, which a single class-plus-band pair cannot express. The donor-specific LOINC code (107914-4) says the antibody is a DSA, so donor-specificity is not restated in a component. The MFI band (DMv1.2 mfi) goes in component[mfi_category]; the measured MFI is a further optional component, for laboratories that report the number.

The result of an anti-HLA antibody screen, donor-specific (DSA) or general (DMv1.2 immunological_data.anti_hla_antibodies, pre_transplant_anti_hla_dsa). A negative screen is a Negative result, never an absent Observation: absence means the screen was not done. The free-text comment on the DM row goes in note.

The Banff 2022 diagnostic category assigned on a kidney allograft biopsy, with the individual Banff lesion scores as components. The category is a conclusion drawn from the lesion scores; recording the scores keeps the biopsy re-readable against a later revision of the classification, which a category alone is not.

Biological sample linked to a transplant visit, aligned with the DMv1.2 bio_sample table. Patient navigable via Specimen.subject. Visit linked via extension[visit_id]. Analysis intent (genomic_sample / epigenomic_sample) is represented as BioSampleAnalysisRequest (ServiceRequest) resources with specimen = Reference(BioSample). send_ingemm_date maps to the native Specimen.receivedTime.

A work order representing the intent to perform omics analysis (genomic or epigenomic) on a BioSample. One instance per analysis type per sample. Analysis intent (genomic_sample / epigenomic_sample) is carried here as ServiceRequest.code; Specimen.type remains free for specimen material type. specimen = Reference(BioSample).

ABO group or Rh factor of the recipient or the donor (DMv1.2 immunological_data.blood_group, rh_factor). One Observation per result. Blood group is a lifelong fact rather than a visit finding, so encounter is optional.

C4d staining of the allograft biopsy by immunohistochemistry or immunofluorescence (DMv1.2 ihc_if_c4d). Recorded once, on the Banff C4d scale, in place of the data model's three overlapping fields: the boolean maps to c4d-0 for negative and c4d-1..3 for positive, and the free-text description goes in note.

One clinical episode for a transplant patient, aligned with the DMv1.2 clinical_event table. The DM's START and END rows for the same episode fold into a single Condition — onsetDateTime from the START row, abatementDateTime from the END row, and both clinical_event_ids in identifier — because two Conditions would make every completed episode count twice. Several Conditions may share an encounter: the DM's visit-to-event 1:1 would make a visit that brings both rejection and CMV unrecordable, and nothing here enforces it. The diagnosis-type events dgf, episodes-aki-after-ltx, histologic-evidence-cni-toxicity and hypoxic-ischemic-event-pltx are ClinicalEvent types (Condition.code from ClinicalEventTypeVS). The coded value vascular_complication_type is in Condition.evidence.code. Non-diagnosis boolean flags (concomitant-medications, treatment-adherence) are ClinicalEventFlagObservation resources. Free-text fields are in Condition.note. Dialysis episodes, retransplantation, and transplant-list entry are linked ClinicalEventProcedure resources via Procedure.reasonReference.

Non-diagnosis boolean flag associated with a clinical event (DMv1.2 clinical_event table): concomitant-medications or treatment-adherence. One per recorded flag: valueBoolean carries the DM value, true or false. A blank DM column produces no Observation.

A procedure sub-event associated with a clinical event (DMv1.2 dialysis episodes, retransplantation, transplant-list entry). Linked to the parent ClinicalEvent Condition via Procedure.reasonReference.

Clinical variables recorded for a transplant patient at a visit, aligned with the DMv1.2 clinical_variable table. Captures weight, height, and diuresis. Concomitant disease(s) are ConcomitantDisease (Condition) resources. Vital signs (BP, HR, O2, temperature) are in the VitalSign profile.

A comorbid or concomitant disease recorded for a transplant patient at a visit (DMv1.2 clinical_variable.concomitant_disease). Represented as a Condition on the patient's problem list. One instance per concomitant disease.

Concomitant medication record for a transplant patient at a visit, aligned with the DMv1.2 concomitant_medication table.

A procedure recorded in the DMv1.2 clinical_variable.concomitant_disease column (ABPM, ERCP, PTCD). These are procedures, so they are Procedure resources rather than ConcomitantDisease Conditions.

DM donor.type: whether the donor was living or deceased at donation. Exactly one per Donor SHALL be recorded. Coded with LOINC 44788-8 Organ donor.

Type of liver graft (complete vs partial) captured as an Observation. Only applicable for liver or combined transplants — invariant pc-donor-1 checks this against the required tx_type extension.

A histopathology report on an allograft biopsy. Carries the same immunological_data_id as the ImmunologicalDataReport built from the same DMv1.2 row, so the row can be reassembled, but keeps its own specimen, date and performer — which a biopsy read weeks after a typing result does not share.

The life of one transplanted graft, from the transplant to graft loss, death or the end of follow-up. Derived from the DMv1.2 transplant row rather than collected: period.start is date_tx, so 'before the transplant' and 'after the transplant' become a date comparison instead of a label on a visit. It also gives the graft an identity of its own, which is what a retransplant needs — a second graft is a second episode, not a flag on the first.

One HLA allele found at one locus, in IMGT/HLA notation. One Observation per allele, not per data-model column: HLA alleles are not ordered, so 'allele 1' and 'allele 2' carry no information, and a fixed pair of slots cannot express a homozygote (one allele), DRB3/4/5 (zero, one or two copies) or a locus typed at more than two fields. Typing resolution is carried by the LOINC code. The subject is the recipient, or the Donor for donor typing.

Groups the immunological results recorded on one DMv1.2 immunological_data row: blood typing, HLA typing, anti-HLA antibodies and ANCA. Each result is its own Observation in result, because one row mixes several tests that have their own specimen, date and performer. The biopsy findings on the same row (banff_category, ihc_if_c4d, if, c4d) become a separate GraftBiopsy carrying the same immunological_data_id. The subject is the recipient, or the Donor for donor-side typing (donor_id); every result SHALL have the same subject as the report.

Immunosuppressive drug catalogue entry. imm_id is carried as an identifier; the drug name maps to Medication.code.

Pharmacokinetic monitoring result (pre-dose trough level, 2 h post-dose level / C2, or AUC) for an immunosuppressant therapy record. Linked to the parent ImmPat MedicationStatement via Observation.partOf. Use Observation.subject to carry the patient directly for FHIR searchability.

Immunosuppressive treatment record for a transplant patient, aligned with the DMv1.2 imm_pat table. The phase — induction, maintenance, or rejection treatment (added by this guide) — is in MedicationStatement.category. The patient is in subject, and is also reachable via context (Visit) → Visit.subject. Pharmacokinetic monitoring values (pre_dose_level, csa_2h_post_dose_level, auc) are represented as linked ImmPatPKObservation resources via Observation.partOf.

Catalogue entry for an instrumental investigation type: one value of the DMv1.2 instrumental_investigation.instrumental_investigation column. The data model has no catalogue table; the performed investigation is PatientInstrumentalInvestigation.

An intraoperative complication that occurred during a transplant procedure (DMv1.2 transplant.intraoperative_complications). Represented as a Condition (encounter-diagnosis) and linked from the Transplant Procedure via Procedure.complicationDetail. One instance per complication. Free-text 'other' complications (intraoperative_complications_other) are carried in Condition.note.

Shared rules for one laboratory result for a transplant recipient, aligned with the DMv1.2 lab_result table. Use one of the specific profiles: LabResultQuantitative for a measured number, or LabResultQualitative for a test whose result is a presence, an absence or an interpretation. A result has either a value or a dataAbsentReason (pc-lab-1).

A laboratory result that is not a number: urine haemoglobin by test strip, schistocytes, the direct antiglobulin test, each of the liver autoantibodies, and the oral glucose tolerance test interpretation. These tests are in LabTestNameVS; their result is a code, not a Quantity.

A laboratory result that is a measured number. The unit has to agree with what the LOINC code measures (pc-lab-2): the same analyte has separate mass and molar codes, and reporting umol/L against a mg/dL code records a different quantity from the one measured. A result below the limit of quantification uses valueQuantity.comparator = '<' rather than a dataAbsentReason.

Definition of a laboratory test, aligned with the DMv1.2 lab_test table: which test, in which unit, and — where the study has agreed them — the reference intervals a result is judged against. Paediatric intervals are age-dependent, so qualifiedInterval carries an age range per interval; without them a result cannot be called normal or abnormal at all, and applying an adult range to a child is wrong in a direction that looks plausible.

Linkage: lab_result.lab_test_id is represented by the shared code, not a reference. R4 Observation.basedOn cannot point at an ObservationDefinition; R5 adds Observation.instantiatesCanonical for exactly this, and that is the link to use at migration. Until then a result and its definition are matched on Observation.code = ObservationDefinition.code, both bound to LabTestNameVS.

The Banff Rejection Activity Index (RAI) for acute liver allograft rejection: the sum of three 0–3 scores — portal inflammation, bile duct inflammation/damage and venous endothelial inflammation — giving a total of 0–9 (3–4 mild, 5–6 moderate, 7–9 severe). The DMv1.2 model has no field for liver rejection grading at all; without it a liver recipient's rejection biopsy cannot be graded, since the Banff categories are the kidney classification.

One blood or urine culture. Record the organism (SNOMED CT) when known; when only the DM positivity flag is available, use the LOINC answer Positive or Negative.

An infection-related diagnosis identified through microbiology/histology in a transplant recipient (DMv1.2 microbiology.ebv_hepatitis_liver, evidence_bkvan). Represented as a Condition. EBV hepatitis applies to liver/combined transplants; BK virus-associated nephropathy (BKVAN) to kidney/combined.

One qualitative viral DNA detection result (e.g. BK virus DNA in urine: detected). When a viral load is available, record MicrobiologyViralLoad instead.

Groups the microbiology results recorded for one person at one visit (one DM microbiology row). Each test is its own Observation in result. The subject is the recipient, or the Donor for donor results; every result SHALL have the same subject as the report. A row with no test columns (only other_positivity or a diagnosis flag) is still a report, with no results, so its microbiology_id is kept.

Shared rules for a single microbiology test result. Use one of the specific profiles: MicrobiologySerology, MicrobiologyNucleicAcid, MicrobiologyViralLoad or MicrobiologyCulture. A result has either a value or a dataAbsentReason (pc-lab-1); an unknown or not-performed test uses dataAbsentReason, and a blank DM column produces no Observation.

One qualitative antibody result (e.g. CMV IgG positive).

One quantitative viral load. Results below the limit of quantification use valueQuantity.comparator = '<'. interpretation carries detected / not detected when the DM *_dna flag is also present.

Panel Observation for donor age at donation (DMv1.2 donor.age_years, age_months). Category is #survey to distinguish from laboratory results. One instance per donor. The recipient is not a subject: the DM patient table records year and month of birth, which are Patient.birthDate.

Instrumental investigation performed on a transplant patient, aligned with the DMv1.2 instrumental_investigation table. All DM fields map to native Observation elements — no extensions.

Panel Observation for pre-transplant immunological scalar facts: maximum PRA, most recent PRA, and histological diagnosis date. Category is #laboratory. One instance per transplant recipient. ABO/Rh typing is in BloodGroupObservation and HLA typing in HlaTyping.

Primary disease that led to transplantation (diag_primary_disease, date_diag_primary_disease). A single profile for both liver and renal primary disease; the affected organ is given in Condition.bodySite. date_diag_primary_disease maps to Condition.onsetDateTime.

Pre-transplant antihypertensive treatment and other medications from a DMv1.2 pre_medication row (antihypertensive_treatment, other_medications). Rituximab and antiviral prophylaxis from the same row are sibling PreMedicationRituximabAntiviral records.

Rituximab desensitisation or antiviral prophylaxis given (or explicitly not given) before transplant: one record per drug, from the pre_medication row. It shares the row's pre_medication_id and visit with the antihypertensive PreMedication but does not reference it. status #completed = given; status #not-taken = explicitly not given.

A PROTECT-CHILD participating transplant centre. center_no (1–4) is carried as identifier.value in the study-centre namespace. All PatientTransplant resources reference their centre via Patient.managingOrganization.

Procedure profile representing a transplant, aligned with the DMv1.2 transplant table. The donor is linked via extension[donor_id]. The associated Visit is linked natively via Procedure.encounter. Intraoperative details are represented as a single TransplantDetails panel Observation linked via Observation.partOf.

The inpatient admission during which the transplant was performed. Derived from the DMv1.2 transplant row, not collected as a visit: the data model has only one visit covering work-up, surgery and the post-operative period, so the surgery, the induction immunosuppression and any post-operative event were all recorded against a visit typed 'pre-transplant'. Separating the admission lets the pre-transplant visit end where the transplant begins, so a pre-transplant analysis stops picking up post-operative data.

A surgical anastomosis performed as part of a transplant procedure (DMv1.2 transplant.type_surgical_biliary_anastomosis, type_ureteral_graft_anastomosis, other_type_ureteral_graft_anastomosis). Modelled as a Procedure linked to the transplant via Procedure.partOf, matching the OMOP PROCEDURE_OCCURRENCE representation. Biliary anastomoses apply to liver/combined transplants; ureteral anastomoses to kidney/combined. Free-text 'other' ureteral anastomosis types are carried in Procedure.code.text.

Intraoperative and peri-operative details panel for a transplant, aligned with the DMv1.2 transplant table. Non-organ-specific detail fields are components of a single Observation linked to the Transplant Procedure via Observation.partOf. One instance per transplant. Organ-specific surgical fields are modelled separately: anastomoses as TransplantAnastomosis (Procedure) via Procedure.partOf, and intraoperative complications as IntraoperativeComplication (Condition) via Procedure.complicationDetail.

Transplant donor profile based on Patient (EU base), aligned with the DMv1.2 donor table. The Donor is the subject of all donor-side results (ABO/Rh and HLA typing, serology, age); these are never recorded against the recipient. Donor type (living / deceased at donation, DM donor.type) SHALL be recorded as a DonorTypeObservation. Patient.deceasedDateTime is optional; when it is on or before the transplant date, the donor type SHALL be Deceased.

Transplant recipient profile based on Patient (EU base), aligned with the DMv1.2 patient table. managingOrganization (the study centre) is required for recipients and prohibited for donors, which keeps the two Patient profiles distinct. Blood group and Rh are in BloodGroupObservation and HLA typing in HlaTyping, both grouped by ImmunologicalDataReport. birth_year and birth_month are Patient.birthDate as a partial date (YYYY-MM, or YYYY when the month is blank); PRA and histological date are in PatientImmunologyObservation. Primary disease diagnoses are PatientPrimaryDiseaseDiagnosis (Condition).

Encounter profile representing a visit in the transplant follow-up schedule. All clinical resources back-reference this Visit via their native encounter/context element or a slim extension on the resource itself. No extensions are needed on Visit.

Vital signs panel for a transplant patient at a visit, aligned with the DMv1.2 vital_sign table. Captures standard vitals plus ABPM (24-hour ambulatory blood pressure) metrics.

The Visit at which the END row of this clinical episode was recorded. Condition.encounter holds the visit the episode was first recorded at; without this, folding the two DM rows into one Condition would lose the second visit link.

The IMGT/HLA database release the allele name was assigned against (e.g. '3.55'). Allele names are release-specific, so without the release a name cannot be resolved unambiguously later.

Reference to the donor associated with this transplant.

Records the transplant type (liver / kidney / combined) on resources that carry organ-specific data fields (DonorLiverTypeObservation), enabling organ-specific FHIRPath invariants within a single resource.

visit_id — reference to the Visit during which this sample was collected.

ABO blood groups for transplant recipients and donors.

LOINC codes for anti-neutrophil cytoplasmic antibody testing: the general screen, the two immunofluorescence patterns, and the two antigen specificities.

LOINC [Identifier] codes naming the HLA specificity an antibody is directed against. Use the donor-specific code (107914-4) for a DSA and the general code (98006-0) for a non-donor-specific anti-HLA antibody; the per-locus codes may be used where the laboratory reports per locus.

LOINC codes for an anti-HLA antibody screen: the general screen, and the donor-specific (DSA) screen.

Banff C4d score (C4d0–C4d3).

Banff 2022 diagnostic category assigned on a kidney allograft biopsy.

The Banff lesion scores recorded as components of a BanffAssessment.

Types of surgical biliary anastomosis (DMv1.2 transplant.type_surgical_biliary_anastomosis). Liver and combined transplants only.

Allowed analysis type codes for BioSampleAnalysisRequest.code.

Permitted values for an ABO group or Rh factor result.

LOINC codes for ABO group and Rh factor.

Codes for ClinicalEventFlagObservation.code — one per non-diagnosis boolean DM flag on the clinical_event table. valueBoolean carries the DM value, true or false.

#completed for a procedure that took place; #not-done for a DM yes/no column recorded as false (retransplantation).

Allowed procedure types for ClinicalEventProcedure.

Allowed clinical event types in the PROTECT-CHILD study (DMv1.2).

Allowed concomitant disease codes in clinical_variable (DMv1.2).

Drugs recordable as concomitant medication. The DMv1.2 concomitant_medication table records only a free-text name, so nothing could be counted, grouped by class or checked for interactions. The binding is extensible and deliberately broad — any ATC code, or a SNOMED CT substance — and the original free text is kept in medicationCodeableConcept.text.

The procedure values of the DMv1.2 clinical_variable.concomitant_disease list: ambulatory blood pressure recording, ERCP and percutaneous transhepatic biliary drainage.

HLA class of an anti-HLA antibody: Class I or Class II.

Qualitative nucleic-acid detection results (LOINC answer codes).

Type of donor liver graft (donor.liver_type: Whole or Split).

Whether the donor was living or deceased when the organ was taken (DM donor.type: Alive → Living, Deceased → Deceased). LOINC answer codes.

LOINC codes for HLA typing, one per locus and typing resolution. Use the resolution-specific code when the laboratory reports the resolution, otherwise the unspecified code. HLA-DP (12285-3) is the migration target for DMv1.2 hla_dp_1/hla_dp_2, whose values are DPB1 alleles at an unrecorded resolution; new data SHOULD use a DPB1 or DPA1 code.

Dose forms that change how an immunosuppressant is dosed or monitored — chiefly immediate-release versus prolonged-release tacrolimus, which have different trough targets and are not interchangeable.

Allowed UCUM dose units for immunosuppressant therapy records (DMv1.2 imm_pat.unit field).

PROTECT-CHILD records the dose given at each administration, not the total for a day. So a DM-sourced record uses one of the plain amount units below and states the frequency in dosage.timing — invariant pc-dose-1 requires it, because '0.1 mg/kg' on its own does not say per dose or per day, and for a twice-daily drug the two differ by a factor of two.

The rate units (…/d) are listed for data from sources that record a daily total, so that such a record can say so rather than being silently mistaken for a per-administration one.

ValueSet of immunosuppressive drug types.

LOINC codes for immunosuppressant pharmacokinetic measurements — trough (C0), 2 h post-dose (C2) and AUC — one per drug. ImmPatPKTypeCS#auc is retained for sirolimus and everolimus, for which LOINC has no AUC code.

The DM column a PK observation came from (pre_dose_level, csa_2h_post_dose_level, auc). Sent as a second coding alongside the LOINC code in ImmPatPKMeasurementVS, so the source column stays explicit without displacing the standard code.

Allowed phase values for MedicationStatement.category on ImmPat records.

ValueSet of instrumental investigation tests conducted.

Allowed intraoperative complications during transplantation.

Allowed UCUM units of measurement for lab result values (DMv1.2 unit field).

Allowed laboratory test names for the PROTECT-CHILD data model. LOINC codes are used as the primary standard; local codes from LabTestLocalCS are used only for calculated or composite measures without a single unambiguous LOINC equivalent.

The three scores that make up the Banff liver Rejection Activity Index.

Mean fluorescence intensity (MFI) band for an anti-HLA antibody.

LOINC codes for blood and urine culture.

Infection-related diagnoses captured in the microbiology table: EBV hepatitis on the liver allograft, and histological evidence of BK virus-associated nephropathy (BKVAN).

LOINC codes for qualitative viral DNA detection in the PROTECT-CHILD microbiology table.

LOINC codes for the serology tests in the PROTECT-CHILD microbiology table. The first code listed for each test is the default; the others are method-, specimen- or donor-specific alternatives.

All PROTECT-CHILD microbiology test codes.

LOINC codes for quantitative viral load. [#/volume] codes are reported in {copies}/mL, [Units/volume] codes in [IU]/mL (invariant pc-vl-1). Whole-blood and serum/plasma codes are distinct because the results are not interchangeable.

The result columns of the DMv1.2 immunological_data table, as DmVariableCS codes. Source value set of ConceptMap DmImmunologicalDataToFhir.

The columns of the DMv1.2 microbiology table, as DmVariableCS codes. Source value set of ConceptMap DmMicrobiologyToFhir.

Allowed results for the instrumental investigation test (Normal, Abnormal).

Allowed antihypertensive drugs for antihypertensive_treatment.

Values for laboratory tests whose result is not a number: presence/absence tests (urine haemoglobin by test strip, schistocytes, the direct antiglobulin test, each liver autoantibody) and interpretations (the oral glucose tolerance test).

Rhesus (Rh) blood group factor: positive or negative.

Qualitative serology results (LOINC answer codes).

Types of surgical anastomosis performed during transplantation — biliary (liver) or ureteral (kidney). Used as Procedure.code on TransplantAnastomosis; free-text 'other' anastomosis types are carried in Procedure.code.text.

Allowed transplant types.

Types of ureteral graft anastomosis (DMv1.2 transplant.type_ureteral_graft_anastomosis). Kidney and combined only.

Types of vascular complication occurring after solid-organ transplantation.

UCUM units for viral load.

Allowed types of visits in the transplant follow-up schedule (DMv1.2).

ABO blood groups for transplant recipients and donors.

Banff C4d score: the extent of C4d staining in peritubular capillaries (kidney) or the portal microvasculature (liver). The DMv1.2 boolean ihc_if_c4d maps to c4d-0 (false) or c4d-1..c4d-3 (true).

Diagnostic categories of the Banff classification of KIDNEY allograft pathology, as revised in the Banff 2022 meeting report. Liver allograft rejection is not graded with these categories — use the Banff Rejection Activity Index (LiverRejectionActivityIndex). See https://banfffoundation.org/.

Intended omics analysis type for a biological sample. Used as the ServiceRequest.code on BioSampleAnalysisRequest resources.

Coded non-diagnosis flags used in ClinicalEventFlagObservation.code to represent boolean DM fields on the clinical_event table. One Observation per recorded flag: valueBoolean carries the DM value, true or false. A blank DM column produces no Observation.

Types of procedures linked to a ClinicalEvent via ClinicalEventProcedure.reasonReference. Used for dialysis episodes, retransplantation, and transplant-list entry (DMv1.2).

Types of clinical events in the PROTECT-CHILD study (DMv1.2 clinical_event_type).

Concomitant disease codes used in the DMv1.2 clinical_variable table. Coded values are carried as ConcomitantDisease (Condition) resources via Condition.code.

HLA class of an anti-HLA (donor-specific) antibody.

Type of liver donation (whole vs split), per donor.liver_type.

Local observation and component codes for graft biopsy scoring: the Banff diagnostic category, the Banff lesion scores, and the liver Banff Rejection Activity Index with its three constituent scores. Neither LOINC nor SNOMED CT carries these.

Local component codes for the anti-HLA antibody profile: HLA class, and the MFI band and value. LOINC has no component code for any of the three.

Local code for the PROTECT-CHILD immunological data report, which groups the results of one DMv1.2 immunological_data row (blood typing, HLA typing, anti-HLA antibodies and ANCA). No single LOINC code covers that mix.

Types of immunosuppressive drugs used in the transplant setting.

Types of pharmacokinetic monitoring observations for immunosuppressant therapy (DMv1.2 pre_dose_level, csa_2h_post_dose_level, auc).

Phase of an immunosuppressant record: induction or maintenance (the DMv1.2 phase values), or rejection treatment (added by this guide). Used as MedicationStatement.category codes.

Types of instrumental investigation tests conducted (expanded for DMv1.2).

Intraoperative complications during transplantation (liver or kidney).

Local codes for laboratory tests that do not have a single unambiguous LOINC code in the PROTECT-CHILD context (e.g., calculated values or composite measures).

Mean fluorescence intensity band for an anti-HLA antibody, as collected by the PROTECT-CHILD data model.

Distinguishes maximum (historical) vs most recent PRA measurements. Used as component codes in PatientImmunologyObservation.

One code per PROTECT-CHILD data-model (DMv1.2) column, as table.column. Used as the source of the DM → FHIR code maps and the DM → OMOP ConceptMaps (codes for the latter are added by scripts/dm-omop-maps.py).

Local codes used only where LOINC or SNOMED CT has no suitable concept: two tests with no LOINC code, and the two infection diagnoses captured in the microbiology table.

The study's own OMOP concepts (vocabulary_id PROTECT-CHILD, concept_id 2000000000 and above), for data-model values that have no standard concept in Athena. Codes are the OMOP concept_id; the ConceptMaps cite them under the OMOP system as they would appear in a PROTECT-CHILD OMOP instance.

Local codes for the free-text components of a patient instrumental investigation (abnormality, other investigation).

Result of the instrumental investigation test conducted (Normal / Abnormal).

Local codes for PROTECT-CHILD patient observation panels and components.

Antihypertensive drugs used as pre-transplant medication.

Rh factor for transplant recipients and donors.

Codes for transplant-level details captured as Observation components.

Type of solid-organ transplant (liver, kidney, combined liver-kidney).

Types of biliary anastomosis used in liver transplantation.

Types of ureteral graft anastomosis used in transplantation (DMv1.2).

Types of vascular complications in transplant (DMv1.2).

Type of visit in the transplant follow-up schedule.

Local codes for vital-sign metrics with no published LOINC code: the vital-signs panel, daytime/night-time mean systolic and diastolic blood pressure, blood pressure load, and nocturnal dip percentages.

Single identifier namespace for PROTECT-CHILD record business identifiers (patient, donor, visit, transplant, and all per-visit clinical/lab/medication/specimen/event records). The resource type distinguishes the kind of record. Identifiers follow one convention: TOKEN-CENTRE-SEQUENCE, for example REC-1-0001 (patient, centre 1, sequence 1) or LBR-1-0006 (lab result); study-wide catalogue entries such as lab tests are not centre-qualified and use TOKEN-SEQUENCE, for example LBT-0001. Identifiers carry no clinical meaning.

Namespace for PROTECT-CHILD study centre identifiers (center_no = 1–4).

Maps the DMv1.2 value list BiliaryAnastomosisTypeCS to the standard codes used by the value sets.

Where each field of the BioSample 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.

Where each field of the ClinicalEvent 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. Not mapped: event_number (calculated; not stored).

Maps the DMv1.2 value list ClinicalEventProcedureTypeCS to the standard codes used by the value sets.

Where each field of the ClinicalEventType 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.

Maps the DMv1.2 value list ClinicalEventTypeCS to the standard codes used by the value sets.

Where each field of the ClinicalVariable 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.

Maps the DMv1.2 value list ConcomitantDiseaseCategory to the standard codes used by the value sets.

Where each field of the ConcomitantMedication 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.

The OMOP concepts for each column of the DMv1.2 bio_sample 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).

Maps a DM boolean *_dna column to the Observation value (or, when *_dna_copies is also present, to the viral-load interpretation DET / ND). A blank column produces no Observation.

Maps a DM boolean serology or culture column to the Observation value. A blank column produces no Observation; an unknown result uses dataAbsentReason.

The OMOP concepts for each column of the DMv1.2 clinical_event 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).

The OMOP concepts for each column of the DMv1.2 clinical_event_type 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).

The OMOP concepts for each column of the DMv1.2 clinical_variable 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).

The OMOP concepts for each column of the DMv1.2 concomitant_medication 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).

The OMOP concepts for each column of the DMv1.2 donor 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).

The OMOP concepts for each column of the DMv1.2 imm_pat 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). Pending (not yet in Athena): pre_dose_level (115766-8); auc (115789-0).

Maps each result column of the DMv1.2 immunological_data table to the code of the resource it becomes. The row itself becomes an ImmunologicalDataReport, and the biopsy columns a GraftBiopsy carrying the same immunological_data_id. Three columns have no code of their own: if becomes GraftBiopsy.conclusion, c4d becomes C4dStain.note, and the free text of pre_transplant_anti_hla_dsa becomes AntiHlaAntibodyScreen.note. The HLA columns are marked wider because each maps to a locus code shared by both allele columns: one Observation per allele replaces the ordered pair of slots.

The OMOP concepts for each column of the DMv1.2 immunological_data 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).

The OMOP concepts for each column of the DMv1.2 immunosuppressant 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).

The OMOP concepts for each column of the DMv1.2 instrumental_investigation 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).

The OMOP concepts for each column of the DMv1.2 lab_result 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).

The OMOP concepts for each column of the DMv1.2 lab_test 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).

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.

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).

The OMOP concepts for each column of the DMv1.2 patient 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).

The OMOP concepts for each column of the DMv1.2 pre_medication 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).

The OMOP concepts for each column of the DMv1.2 transplant 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).

The OMOP concepts for each column of the DMv1.2 visit 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).

The OMOP concepts for each column of the DMv1.2 vital_sign 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).

Where each field of the Donor 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.

Maps the DMv1.2 value list DonorLiverTypeCS to the standard codes used by the value sets.

Where each field of the ImmPat 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.

Where each field of the Immunological Data 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.

Where each field of the Immunosuppressant 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.

Maps the DMv1.2 value list ImmunosuppressantDrugTypeCS to the standard codes used by the value sets.

Where each field of the InstrumentalInvestigation 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.

Maps the DMv1.2 value list InstrumentalInvestigationNameCS to the standard codes used by the value sets.

Maps the DMv1.2 value list IntraoperativeComplicationCS to the standard codes used by the value sets.

Where each field of the LabResult 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.

Where each field of the LabTest 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.

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.

Maps the DMv1.2 value list MicrobiologyCS to the standard codes used by the value sets.

Where each field of the Patient 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.

Where each field of the PreMedication 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.

Maps the DMv1.2 value list PreMedicationAntihypertensiveDrugCS to the standard codes used by the value sets.

Where each field of the Transplant 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.

Maps the DMv1.2 value list TransplantTypeCS to the standard codes used by the value sets.

Maps the DMv1.2 value list UreteralAnastomosisTypeCS to the standard codes used by the value sets.

Maps the DMv1.2 value list VascularComplicationTypeCS to the standard codes used by the value sets.

Where each field of the Visit 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.

Where each field of the Vital Sign 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.

DM blood_bkv_dna = false.

DM urine_bkv_dna = false.

DM cmv_dna = false.

DM cmv_igg = true.

DM cmv_igm = false.

Donor cmv_igg = true (donor-specific LOINC code).

Donor cmv_igm = false (donor-specific LOINC code).

Donor ebv_igg_ebna = true. LOINC has no donor-specific EBNA IgG code, so the general code is used; the Donor subject marks it as a donor result.

Donor ebv_igg_anti_vca = true (donor-specific LOINC code).

DM ebv_igg_ebna = true.

DM ebv_igg_anti_vca = true.

DM ebv_igm_anti_vca = false.

DM ebv_igm_anti_ea = false. Local code: LOINC has no IgM-specific early-antigen test.

DM ebv_dna = true and ebv_dna_copies = 2450 → one viral-load Observation, interpretation Detected.

12-month post-transplant follow-up visit for recipient REC-1-0001. The vital-sign panel and the creatinine result recorded at the 1-month visit repeat here — the shape follow-up data takes across the study timeline.

6-month post-transplant follow-up visit. The concomitant medication in progress since January and the abdominal imaging performed for the follow-up are recorded against this visit.

Example biological sample aligned with DMv1.2. genomic_sample=true, epigenomic_sample=false.

Non-diagnosis boolean flag associated with the clinical event: treatment adherence recorded as true (valueBoolean = true). It links to its parent ClinicalEvent via Observation.focus.

Hemodialysis episode linked to a clinical event via reasonReference.

Acute kidney injury in the first week after liver transplantation, requiring temporary renal replacement therapy. It starts during the transplant admission and is closed at the 1-month visit, so the two DM rows fold into one Condition. Because the transplant admission is its own Encounter, this post-operative event is not filed under a visit typed 'pre-transplant'.

One rejection episode, not two records. The DM START row (CLE-1-0002, recorded at the unscheduled clinical-event visit) and the END row (CLE-1-0004, recorded at the 6-month visit) fold into this single Condition: both identifiers are kept, onset and abatement carry the two dates, and the END visit is in extension[endVisit]. Counting rejections over this bundle returns one, not two.

Example clinical variables for a transplant patient at a 1-month follow-up visit (DMv1.2).

Example concomitant disease (hypertension) recorded for a transplant patient at a follow-up visit (DMv1.2).

Example ongoing concomitant antihypertensive medication (DMv1.2).

DM clinical_variable.concomitant_disease = ERCP, recorded as a Procedure.

Tacrolimus trough level (C0) linked to the maintenance ImmPat record via partOf.

Tacrolimus reduced from 0.1 to 0.06 mg/kg after EBV reactivation — the first-line response, and what leaves the graft exposed to the rejection two months later.

Methylprednisolone pulse, 10 mg/kg/day for three days, for the November rejection episode. Recorded under the rejection-treatment phase and pointing at the episode it treated, so it can be told apart from the patient's background immunosuppression. The dose is an amount per administration with a once-daily dosage.timing (pc-dose-1), so the daily exposure is stated rather than inferred.

Methylprednisolone as an immunosuppressant catalogue entry.

Example induction immunosuppressant record (methylprednisolone) at time of transplant.

Example maintenance immunosuppressant record (tacrolimus) at the 1-month visit. PK monitoring values are separate ImmPatPKObservation resources linked via Observation.partOf.

Tacrolimus (FK506) catalogue entry, referenced by the maintenance ImmPat records in both worked examples.

Example instrumental investigation catalogue entry — Liver Doppler ultrasound.

Example intraoperative complication (major bleeding) linked to the example transplant via Procedure.complicationDetail.

Example creatinine result for a transplant recipient.

Creatinine repeated at 12 months. Improved from 1.2, but 0.8 mg/dL is still above the paediatric reference range (~0.4–0.7), so it is flagged H — do not apply adult ranges.

ALT at the rejection visit. The rise from 86 to 210 U/L prompts the graft biopsy.

Alanine aminotransferase result for recipient REC-1-0001 at the 1-month follow-up visit.

Alanine aminotransferase result for recipient REC-1-0001 at the 12-month follow-up visit.

Albumin result for recipient REC-1-0001 at the 1-month follow-up visit.

Albumin result for recipient REC-1-0001 at the 12-month follow-up visit.

GGT at the rejection visit — the cholestatic component, with the bilirubin.

Total bilirubin at the rejection visit, raised with the transaminases and GGT.

Example lab test catalogue entry — Albumin, reported in g/dL.

Serum creatinine in mg/dL, with age-banded reference intervals. The intervals below are ILLUSTRATIVE, to show the structure — PROTECT-CHILD has not agreed reference intervals, and each centre's laboratory may use its own. Until the study settles that, results are not comparable across centres, which is the point this catalogue entry exists to make visible.

Example microbiology diagnosis — EBV-associated hepatitis of the liver allograft.

Serology of the deceased donor DON-1-0001 at procurement: CMV IgG and EBV IgG positive (D+). The Donor is the subject of the report and of every result, so these never mix with the recipient's serostatus; the record is kept at the recipient's pre-transplant visit (visit_id). Donor-specific LOINC codes are used where LOINC has them.

Microbiology row MIC-1-0001: EBV viral load and serology, CMV and BK virus surveillance. Each test is its own Observation.

Example liver Doppler ultrasound result for a transplant recipient.

Liver biopsy taken when EBV DNA was detected. EBV hepatitis is a histological diagnosis — serology and viral load cannot separate it from rejection. Evidence for MicrobiologyDiagnosisExample1.

Pre-transplant antihypertensive field, recorded as #not-taken against the drug class rather than a named agent: none was needed, as children with cirrhosis often have low-normal blood pressure. Naming a specific agent such as amlodipine as not-taken would imply that agent was considered. Her hypertension appears after transplant — see ConcomitantDiseaseExample1.

Rituximab from the same pre_medication row as PreMedicationExample1: same identifier and visit, no reference between them. effectiveDateTime is the last dose (date_last_rituximab). Waiting-list desensitisation of a sensitised candidate (peak PRA 80%), not directed at a particular donor — the graft came from a deceased donor.

Example biliary anastomosis (duct-to-duct) performed as part of the example liver transplant, linked via Procedure.partOf.

Example transplant details panel for a liver transplant (DMv1.2).

Example vital signs panel for a transplant recipient at the 1-month visit.

The same vital-signs panel repeated at the 12-month follow-up visit, showing how a panel recurs across the visit timeline.

Unscheduled visit prompted by the acute rejection episode. The rejection Condition, its treatment-adherence flag and the biopsy immunology panel are all recorded against this visit.

Age at donation for the transplant donor (PatientDemographicsObservation; subject = Reference(Donor)).

Partial (reduced-size) liver graft — a whole adult liver would be large-for-size for a 32.5 kg recipient.

DM donor.type = Deceased for DON-1-0001.

ServiceRequest representing genomic_sample = true for BioSampleExample1.

Biopsy of the liver allograft at the rejection episode. It carries the same immunological_data_id as ImmReportRejection1, which holds the antibody results from the same DM row, but its own specimen and date.

The life of the liver graft transplanted on 15 August 2023. Everything dated before period.start is pre-transplant, whatever a visit is labelled.

The serology half of the rejection work-up: one de novo donor-specific antibody, and a negative ANCA. The biopsy findings recorded on the same DM row are in GraftBiopsyLiver1, which carries the same immunological_data_id.

ABO/Rh and HLA typing of the deceased donor DON-1-0001. The Donor is the subject, so this typing never appears among the recipient's own results. B*08:01 is the mismatched allele the de novo DSA is directed against.

One DMv1.2 immunological_data row: ABO/Rh group, the full HLA typing in IMGT/HLA notation, and the pre-transplant anti-HLA antibody screen for recipient REC-1-0001.

Primary liver disease diagnosis leading to transplantation.

PRA and histological diagnosis date for the recipient (PatientImmunologyObservation).

Pre-transplant (baseline) visit for recipient REC-1-0001: the desensitisation work-up, the PRA and HLA typing, the donor typing and serology, and the pre-transplant medication. It ends the day before surgery — the admission is TransplantAdmissionExample1, so nothing post-operative is filed under a visit typed 'pre-transplant'.

Example transplant instance mapped from the DMv1.2 transplant table.

The inpatient stay for the liver transplant: surgery on 15 August with its anastomosis and intraoperative bleed, induction immunosuppression the same day, and the day-5 acute kidney injury with its dialysis. Discharged on 28 August.

Deceased donor (see DonorTypeExample1). The date of death, 14 August 2023, is known here and falls before the transplant on 15 August 2023, consistent with the Deceased donor type.

Example transplant recipient REC-1-0001 (DMv1.2 patient table) conforming to PatientTransplant.

Example visit. Clinical resources (ClinicalVariable, Microbiology, PreMedication, etc.) carry the back-reference to this Visit via their own .encounter / .context element or extension.

Negative ANCA.

Diffuse C4d staining (C4d3). The data model's boolean ihc_if_c4d = true would have lost the extent.

Positive ASMA. Under the composite code this and the negative ANA above were one field with one answer.

One of the nine antibodies the data model's single 'liver autoantibodies' field collapsed together. Negative here, and the result says which antibody was negative.

The same analyte as LabResultObservationExample2, reported the way a European laboratory reports it. It carries the molar LOINC code 14682-9, not the mass code 2160-0 — pc-lab-2 rejects µmol/L against the mass code.

A class I DSA against the donor's mismatched B*08:01 (see ImmReportDonor1). The specificity is the value of the observation, so the antibody can be matched against the donor's typing automatically; the DM band SR is kept, and the measured MFI is recorded alongside it.

HLA-A allele A*01:01.

HLA-A allele A*02:01.

Donor ABO group O — compatible with the group A recipient.

HLA-B allele B*08:01.

HLA-B allele B*44:03.

HLA-C allele C*07:01.

HLA-C allele C*16:01.

HLA-DQB1 allele DQB1*02:01.

HLA-DQB1 allele DQB1*02:02.

HLA-DRB1 allele DRB1*03:01.

HLA-DRB1 allele DRB1*07:01.

Donor Rh positive.

eGFR at the 12-month visit. The formula is the code: Schwartz is the paediatric creatinine-based formula, so no free-text formula field is needed — and MDRD, which the OMOP crosswalk pointed at, is an adult formula that is not valid in a child.

RAI 6 of 9 (moderate acute rejection): portal inflammation 3, bile duct inflammation 2, venous endothelial inflammation 1. The DMv1.2 model has no field for this, so a liver recipient's rejection could not be graded at all.

Percutaneous biopsy of the liver allograft taken at the rejection episode.

Negative pre-transplant screen. The negative result is recorded: an absent Observation would mean the screen was not done.

HLA-A allele A*02:01.

HLA-A allele A*24:02.

Recipient ABO group A.

HLA-B allele B*07:02.

HLA-B allele B*44:03.

HLA-C allele C*07:02.

HLA-C allele C*16:01.

HLA-DPB1 allele DPB1*02:01.

HLA-DPB1 allele DPB1*04:01.

HLA-DQB1 allele DQB1*02:01.

HLA-DQB1 allele DQB1*06:02.

HLA-DRB1 allele DRB1*03:01.

HLA-DRB1 allele DRB1*15:01.

Recipient Rh positive.

First scheduled follow-up after transplantation. The CRF groups a brain MRI (11 October) and the month-1 blood tests (5 November) under this visit.

Mean 24-hour blood pressure 99/77 mmHg from the ambulatory recording.

ALT 45 U/L, flagged high.

AST 43 U/L.

GGT 258 U/L, flagged high.

LDH 365 U/L, flagged high. Method not stated, so the method-less code is used.

Abdominal ultrasound at the recipient work-up: normal.

Albumin 4.9 g/dL.

ABPM at the PRES visit. ABPM is one of the procedure values of the DM's concomitant_disease list; the 24-hour means are in KidneyVitalSignEvent1.

Arterial hypertension since January 2017, recorded at the pre-transplant visit and still active at the PRES event.

Brain MRI on 11 October 2018: bilateral parieto-occipital signal change, a month before PRES was recorded.

Calcium 10.7 mg/dL, flagged high.

Cholesterol 248 mg/dL.

Weight and height at the recipient work-up. Anaemia is not in the DM's concomitant-disease list, so it goes in other_concomitant as free text.

Unscheduled visit at which posterior reversible encephalopathy syndrome was recorded.

Serum creatinine 2.78 mg/dL, flagged high.

Cystatin C 4.51 mg/L. The source says mg/dL, which would be about forty times the upper limit; mg/L matches the eGFR of 17.

HLA-A A24, typed at low resolution (source: 'A (24, 30)').

HLA-A A30, low resolution.

Donor ABO group O — identical to the recipient.

HLA-B B7, low resolution (source: 'B (07, 14)').

HLA-B B14, low resolution.

Donor cmv_igg = true (donor-specific LOINC code).

Donor cmv_igm = false (donor-specific LOINC code).

HLA-DRB1 DR4, low resolution (source: 'DR (04, 15)').

HLA-DRB1 DR15, low resolution.

Donor ebv_igg_ebna = true. LOINC has no donor-specific code for this test.

Donor ebv_igg_anti_vca = true (donor-specific LOINC code).

Donor ebv_igm_anti_vca = false. LOINC has no donor-specific code for this test.

Donor ebv_igm_anti_ea = false. Local code: LOINC has no IgM-specific early-antigen test.

Donor Rh positive.

Age of donor DON-2-0001 at donation: 29 years.

EBV and CMV serology of donor DON-2-0001: EBV past infection (VCA IgG and EBNA IgG positive, both IgM negative) and CMV IgG positive. The DM's cmv_dna column is blank, so there is no CMV DNA result: a blank column produces no resource.

DM donor.type = Alive for DON-2-0001.

ABO/Rh and low-resolution HLA typing of donor DON-2-0001: A24, A30; B7, B14; DR4, DR15. The Donor is the subject, so none of this appears among the recipient's results.

Creatinine-based eGFR 13.2 mL/min/1.73 m². The value is bedside Schwartz (0.413 × 89 cm / 2.78 mg/dL), so the Schwartz code is used.

Cystatin C-based eGFR 17 mL/min/1.73 m², flagged low. The formula is carried by the LOINC code.

Echocardiogram at the recipient work-up: normal.

Erythrocytes 3.58 × 10⁶/µL, sent as 3.58 × 10¹²/L: the same quantity in a unit the catalogue lists.

Glucose 80 mg/dL.

Haematocrit 34.6 %.

Haemoglobin 10.7 g/dL.

Leukocytes 16.86 × 10³/µL.

Living donor for recipient REC-2-0001, aged 29 at donation. Contrast with the deceased donor in the liver example.

Methylprednisolone (Urbason) 4 mg once a day, recorded at the month-1 visit. No start date in the source.

Tacrolimus (FK506) 2 mg every 12 hours, recorded at the month-1 visit. The source gives no start date, so effective[x] is omitted rather than guessed.

Phosphate (phosphorus) 6.3 mg/dL, flagged high.

Platelets 694 × 10³/µL, flagged high.

PRES on 10 November 2018, in a hypertensive child on tacrolimus: the drug-toxicity outcome the study tracks. No end date is in the source, so the episode stays active.

Potassium 5.1 mmol/L.

Pre-transplant work-up for recipient REC-2-0001: the donor work-up in May and the recipient work-up in September 2018. The admission is KidneyTransplantAdmission1.

End-stage chronic kidney disease secondary to right renal cystic dysplasia, diagnosed in March 2015 at one month of age. The dysplasia is the coded cause; the DM's free text is kept in note.

Recipient ABO group O.

Paediatric kidney transplant recipient at the University of Padova (centre 2). DM birth_year 2015 and birth_month 2 give the partial birthDate 2015-02.

Recipient Rh positive.

Recipient ABO group O, Rh positive, typed at diagnosis in March 2015 and recorded at the pre-transplant visit. The source has no recipient HLA typing, so there are no HlaTyping results.

Sodium 136.4 mmol/L.

The life of the kidney graft transplanted on 30 September 2018, from a living donor.

Living-donor kidney transplantation for recipient REC-2-0001 on 30 September 2018.

Total bilirubin below 0.10 mg/dL: a comparator, not a dataAbsentReason, because the result is known to be under the limit.

The inpatient stay for the transplant on 30 September 2018. The discharge date is not in the source, so period.end is omitted.

Cold ischemia 92 minutes, warm ischemia 6 minutes, 42 months from diagnosis to transplant, and the vascular anastomosis redone for poor graft perfusion.

Urea 208 mg/dL, flagged high. Urea, not urea nitrogen.

Uric acid 7.6 mg/dL, flagged high.

Urine protein/creatinine ratio 0.19 mg/mg (DM lab test 'Proteinuria/creat. ratio', local code).

Blood pressure, heart rate, oxygen saturation and temperature at the recipient work-up.

La Paz University Hospital, Madrid, Spain (center_no = 1).

University of Padova, Italy (center_no = 2).

IRCCS ISMETT, Palermo, Italy (center_no = 3).

University Medical Centre Hamburg-Eppendorf, Germany (center_no = 4).

A paediatric kidney transplant recipient (REC-2-0001, Padova) from the donor and recipient work-up through a living-donor transplant and the month-1 visit to posterior reversible encephalopathy syndrome on tacrolimus — assembled as one collection Bundle in which every internal reference resolves. Based on the Patient 01 timeline of the WP2 data-model presentation.

A single paediatric liver transplant recipient (REC-1-0001, La Paz) from enrolment through donor, transplant, intraoperative findings, follow-up visits, labs, biospecimen, immunosuppression, microbiology and post-transplant clinical events — assembled as one collection Bundle in which every internal reference resolves.