Logical model representing the PROTECT-CHILD data model entity bio_sample.

Logical model representing the PROTECT-CHILD data model entity clinical_variable.

Logical model representing the PROTECT-CHILD data model entity concomitant_disease.

Logical model representing the PROTECT-CHILD data model entity concomitant_episode.

Logical model representing the PROTECT-CHILD data model entity concomitant_medication.

Logical model representing the PROTECT-CHILD data model entity donor.

Logical model representing the PROTECT-CHILD data model entity epigenome_study.

Logical model representing the PROTECT-CHILD data model entity genomic_test.

Logical model representing the PROTECT-CHILD data model entity imm_ind_pat.

Logical model representing the PROTECT-CHILD data model entity imm_main_pat.

Logical model representing the PROTECT-CHILD data model entity immunosuppressant.

Logical model representing the PROTECT-CHILD data model entity instrumental_investigation.

Logical model representing the PROTECT-CHILD data model entity lab_result.

Logical model representing the PROTECT-CHILD data model entity lab_test.

Logical model representing the PROTECT-CHILD data model entity mark_imm_func.

Logical model representing the PROTECT-CHILD data model entity methylomic_study.

Logical model representing the PROTECT-CHILD data model entity microbiology.

Logical model representing the PROTECT-CHILD data model entity outcome.

Logical model representing the PROTECT-CHILD data model entity outcome_type.

Logical model representing the PROTECT-CHILD data model entity pat_inst_inv.

Logical model representing the PROTECT-CHILD data model entity patient.

Logical model representing the PROTECT-CHILD data model entity post_event.

Logical model representing the PROTECT-CHILD data model entity post_event_type.

Logical model representing the PROTECT-CHILD data model entity pre_medication.

Logical model representing the PROTECT-CHILD data model entity reference_genome.

Logical model representing the PROTECT-CHILD data model entity target_region.

Logical model representing the PROTECT-CHILD data model entity transplant.

Logical model representing the PROTECT-CHILD data model entity unit.

Logical model representing the PROTECT-CHILD data model entity variant_annotation.

Logical model representing the PROTECT-CHILD data model entity variant_occurrence.

Logical model representing the PROTECT-CHILD data model entity visit.

ABO blood group as an Observation (LOINC 883-9). Reusable for both recipients and donors.

Biological sample linked to transplant patients and omics studies, aligned with the bio_sample table.

Clinical variables and vital signs recorded for a transplant patient.

Relevant concomitant diseases associated to a subject or record.

Clinical episode related to a concomitant disease for a transplant patient.

Concomitant medication records associated with a concomitant episode.

Type of liver graft (complete vs partial) captured as an Observation (LOINC 74836-8).

Dialysis method prior to kidney transplantation (LOINC 70958-4).

Epigenome (e.g. methylation array) study metadata and platform details.

Definition of a genomic test / sequencing platform and pipeline configuration.

HLA Class I (A, B, C) typing as an Observation panel (LOINC 96629-1).

HLA Class II (DP, DQ, DR) typing as an Observation panel (LOINC 96640-8).

Date of histological diagnosis captured as an Observation date result (LOINC 77975-1).

Immunosuppressive drug definition used in initial or maintenance therapy.

Record of immunosuppressive induction treatment given to a transplant patient.

Maintenance immunosuppressive therapy given to the transplant patient, aligned with the immunosuppressive_maintenance_patient table.

Catalogue of instrumental investigation tests, aligned with the instrumental_investigation table.

Individual laboratory result for a transplant recipient, aligned with the lab_result table.

Definition of a laboratory test, including its name and unit.

Laboratory report grouping one or more lab result observations for a transplant recipient.

Primary liver disease diagnosis. Use effectiveDateTime as the diagnosis date and valueCodeableConcept as the diagnosis.

Markers of immune function including HLA and non-HLA antibodies for a transplant patient.

Methylomic study / locus-level methylation metrics.

Microbiology results related to transplant recipients and/or donors, aligned with the microbiology table.

Outcome information for transplant patients, linked to multiple clinical domains.

Definition of an outcome type used to categorize outcome records.

Panel reactive antibody / cPRA as an Observation (LOINC 80737-0). Use Observation.method to mark max vs last.

Instrumental investigation performed on a transplant patient, aligned with the patient_instrumental_investigation table.

A curated list of patient-level observations (ABO, Rh, PRA, HLA typing, diagnoses, etc.) that reference a transplant recipient.

Clinical events occurring after transplant, associated with a patient and event type.

Definition of a post-transplant event type.

Pre-transplant medication record aligned with the pre_medication table.

Reference genome definition used by genomic tests, including build_name and FASTA path.

Primary renal disease diagnosis. Use effectiveDateTime as the diagnosis date and valueCodeableConcept as the diagnosis.

Rh type as an Observation (LOINC 10331-7). Reusable for both recipients and donors.

Target gene / genomic region associated with a genomic test platform.

Encounter profile representing a transplant, linking the transplant recipient and donor and aligned with the transplant table.

Transplant donor profile based on the FHIR Patient resource, aligned with the donor table.

Transplant recipient profile based on the FHIR Patient resource, aligned with the patient table.

Annotation of a variant occurrence using external databases and classifications.

Variant occurrence information within a target region.

Encounter profile representing a visit in the transplant follow-up schedule, aligned with the visit table.

csa2h_post_dose_level – drug level measured 2 hours after dosing (commonly cyclosporine C2).

Anti-endothelial cell antibodies or other non-HLA antibodies not captured above.

Angiotensin II type-1 receptor (AT1R) antibody result.

adenovirus_igg – presence of IgG antibodies to adenovirus; false=Negative, true=Positive.

adenovirus_igm – presence of IgM antibodies to adenovirus; false=Negative, true=Positive.

Age (in years) of the subject at the time of DNA extraction.

Name and version of the alignment tool.

Allele frequency for the variant.

Variant allele sequence (e.g., C).

Database used for this variant annotation.

Information about the databases used for annotation.

Information about the tool used for annotation.

Anti-MICA (MHC class I–related chain A) antibody result.

Anti-MICB (MHC class I–related chain B) antibody result.

antihypertensive_treatment – blood-pressure–lowering drug(s) used pre-transplant.

antiviral_phrophylaxis – preventive antiviral medication(s) given to reduce risk of viral infection or reactivation (Kidney only).

auc – pharmacokinetic area under the curve for the immunosuppressant.

Date when the array was run.

bkv_fish_kidney_biopsy – BK virus FISH on kidney biopsy; false=Negative, true=Positive.

bkv_dna_kidney_biopsy – detection of BK virus DNA on kidney biopsy; false=Negative, true=Positive.

Beta value representing methylation level.

Reference to the primary biosample collected at this visit (bio_sample_id).

Date of bisulfite conversion.

Bisulfite conversion kit used in the epigenome experiment.

blood_bkv_dna – detection of BK virus DNA in blood; false=Negative, true=Positive.

cmv_dna – CMV nucleic acid test result (false=Negative, true=Positive).

ebv_dna – EBV nucleic acid test result (quantitative, float).

parvovirus_b19_dna – detection of parvovirus B19 DNA in blood; false=Negative, true=Positive.

cmv_igg – presence of IgG antibodies against CMV; false=Negative, true=Positive.

cmv_igm – presence of IgM antibodies against CMV; false=Negative, true=Positive.

Locus information for CNV.

Type of chip used for the epigenome array.

Chromosome identifier (e.g. 1–22, 23=X, 24=Y, 25=MT).

Coordinate system for numbering the chromosomes.

Reference to clinical variable/vital signs information associated with this outcome.

Reference to clinical variables recorded at this visit (clinical_variable_id).

Cold ischaemia time for the graft in minutes (cold_ischemia_time).

Reference to the concomitant disease record associated with this episode.

Set of relevant concomitant diseases.

Reference to the concomitant episode this medication belongs to.

Reference to concomitant episode information associated with this outcome.

Reference to a concomitant episode associated with this visit (concomitant_episode_id).

Copy number value for CNV data.

dna_concentration – DNA concentration for the sample (float).

Date when vital signs were measured.

Date on which the instrumental investigation was performed.

Detection p-value for the methylation measurement.

Diastolic blood pressure in mmHg.

donor_id – reference to the donor associated with this microbiology record.

Whether the donor is living or deceased.

Donor-specific antibody flag for the HLA antibody above (yes/no).

Ratio of donor graft weight to recipient body weight (d_r_weight_ration).

dose – maintenance dose of the immunosuppressant.

ebv_igg_ebna – presence of IgG antibodies against EBV Nuclear Antigen (EBNA); false=Negative, true=Positive.

ebv_igg_anti_vca – presence of IgG antibodies against EBV Viral Capsid Antigen (VCA); false=Negative, true=Positive.

ebv_igm_anti_ea – presence of IgM antibodies against EBV Early Antigen (EA); false=Negative, true=Positive.

ebv_igm_anti_vca – presence of IgM antibodies against EBV Viral Capsid Antigen (VCA); false=Negative, true=Positive.

Endothelin receptor type-A (ETAR) antibody result.

Date when this maintenance immunosuppressant regimen was stopped (if applicable).

End position of the target region (genomic coordinate).

epigenome_study_id – reference to epigenome study linked to this sample.

Date of the concomitant episode.

Description of the concomitant episode.

Free-text description of the post-transplant event.

Date when the post-transplant event resolved or ended.

Date when the post-transplant event started.

First warm ischaemia time for the graft in minutes (1_warm_ischemia_time).

Genomic position where a fusion variant occurs.

Supporting read count of the fusion.

Somatic or germline origin of the variant.

genomic_test_id – reference to the genomic test configuration used for this sample.

Name of the platform using sequencing, assigned by the institution.

Version of the platform using sequencing, assigned by the institution.

Reference to the genomic test used in this epigenome study.

Reference to the genomic test (platform) containing this target region.

Allele state.

Gene ID based on HGNC nomenclature.

Gene symbol given by HGNC nomenclature.

Nomenclature for the sequence variant at the DNA level (HGVS c. notation).

Nomenclature for the sequence variant at the protein level (HGVS p. notation).

Class or locus of the HLA antibody being recorded.

hsv_igg – presence of IgG antibodies to HSV; false=Negative, true=Positive.

hsv_igm – presence of IgM antibodies to HSV; false=Negative, true=Positive.

Pulse rate in beats per minute.

Patient’s height/length in centimeters.

Reference to the immunosuppressant drug used for induction.

immunosuppressant_id – reference to the immunosuppressant drug used for maintenance.

Dose of the selected immunosuppressant used for induction.

Name/type of the immunosuppressant drug.

Reference to immunosuppressive induction treatment associated with this visit (imm_ind_pat_id).

Reference to immunosuppressive maintenance treatment associated with this visit (imm_main_pat_id).

instrumental_investigation_id – reference to the catalogue entry describing the test performed.

Name of the instrumental investigation test conducted.

Whether and which complications occurred during surgery (intraoperative_complications).

Transplanted kidney side (kidney_side).

Reference to laboratory results associated with this visit (lab_result_id).

patient_id – reference to the transplant recipient for whom this lab result is recorded.

Reference to lab test definition associated with this outcome.

Name of the laboratory test conducted.

lab_test_id – reference to the lab test definition (LabTest catalog row) associated with this lab result.

M-value transformation of the beta value.

Median Fluorescence Intensity (MFI) for the HLA antibody listed in hla_antibody_class.

Manifest number for the array.

Mean target coverage.

Type of concomitant medication applied.

Medication(s) relevant to this variant annotation.

Number of reads showing methylation.

methylomic_study_id – reference to methylomic study linked to this sample.

Reference to microbiology results associated with this outcome.

Reference to microbiology results associated with this visit (microbiology_id).

Whether the patient’s native kidney was surgically removed before the transplant (nephrectomy_original_kidney).

Specification of other types of complications during surgery (intraoperative_complications_other).

other_medications – any other relevant pre-transplant medications.

Reference to the outcome record associated with this visit (outcome_id).

Date associated with the outcome (e.g. assessment date).

Reference to the type/category of outcome.

Name of the outcome type.

Oxygen saturation at rest, in percent.

parvovirus_b19_dna_igg – presence of IgG antibodies to parvovirus B19; false=Negative, true=Positive.

parvovirus_b19_dna_igm – presence of IgM antibodies to parvovirus B19; false=Negative, true=Positive.

Reference to the patient for whom clinical variables are recorded.

Reference to the patient for whom the concomitant episode is recorded.

Reference to the patient receiving immunosuppressive induction.

Reference to the patient for whom the immune function markers are recorded.

patient_id – reference to the transplant recipient associated with this microbiology record.

Reference to the patient for whom the outcome is recorded.

patient_id – reference to the transplant recipient for whom the instrumental investigation was performed.

Reference to the patient who experienced the post-transplant event.

Reference to patient instrumental investigation associated with this outcome.

Reference to a patient instrumental investigation associated with this visit (pat_inst_inv_id).

Percentage of selected bases covered at ≥100x.

Identifier of the sample pool.

Reference to post-transplant event associated with this outcome.

Reference to the type/category of the post-transplant event.

Name of the post-transplant event type.

Reference to a post-transplant event (e.g. rejection episode) occurring at this visit (post_event_id).

pre_dose_level – drug level measured immediately before dosing (trough level).

Reference to pre-transplant medication information associated with this outcome.

Reference to pre-medication information associated with this visit (pre_medication_id).

patient_id – reference to the transplant recipient for whom the pre-medication is recorded.

Link or identifier to raw data files.

Total number of reads for this locus.

Information about the length of the read.

Information about the method of sequence reading.

patient_id – reference to the transplant recipient for whom maintenance therapy is recorded.

Reference to the reference genome used for this genomic test.

Reference allele sequence (e.g., A).

Filesystem or URI path of the reference genome FASTA file.

Reference to the reference genome used in this methylomic study.

Transcript ID based on a protein-coding RNA (mRNA), including accession and version number.

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

rituximab – any rituximab given pre-transplant.

Device used as SNP reader.

Sample identifier used in the epigenome study.

send_ingemm_date – date when the sample was sent to INGEMM.

Type of sample used in the epigenome study (Blood, Saliva, Other tissues).

Date when the array was scanned.

Second warm ischaemia time for the graft in minutes (2_warm_ischemia_time, kidney only).

Sentrix array barcode.

Position on the Sentrix array.

Structural variant type.

Sequencer machine information.

Date when this maintenance immunosuppressant regimen was started.

Start position of the target region (genomic coordinate).

Systolic blood pressure in mmHg.

Information about the capture method of examined and targeted region.

Identifier of the target disease for this epigenome study.

Identifier of the target region for which methylation information is recorded.

Reference to the target region (gene/region) for which the variant information is recorded.

Body temperature in degrees Celsius.

Months between disease diagnosis and transplant date (time_diag_to_tx).

Reference to the transplant associated with this visit (transplant_id).

Reference to the donor associated with this transplant.

Type of biliary reconstruction used (type_surgical_biliary_anastomosis).

Reference to the unit definition associated with this lab test.

urine_bkv_dna – detection of BK virus DNA in urine; false=Negative, true=Positive.

vzv_igg – presence of IgG antibodies to varicella–zoster virus; false=Negative, true=Positive.

vzv_igm – presence of IgM antibodies to varicella–zoster virus; false=Negative, true=Positive.

Name and version of the variant calling tool.

Classification level for the variant.

Exon number in which the variant occurred.

Functional variant type.

Reference to the variant occurrence this annotation refers to.

Origin of the variant (e.g., inherited, de novo, somatic).

Pathogenicity assessment (e.g., pathogenic, likely pathogenic, VUS, benign).

Variant depth divided by read depth.

Tier level for the variant (e.g., Tier 1, Tier 2).

Presence of relevant arterial/venous anatomical variants (vascular_anomalies).

Whether there is a vessel size/configuration mismatch requiring tailoring (vessel_mismatch_d_r).

Patient’s weight in kilograms.

dbSNP reference ID (rsID) maintained by NCBI.

ABO blood groups for transplant recipients and donors.

Allowed tissue types for BioSample.tissue_type.

ValueSet of relevant concomitant diseases.

ValueSet of concomitant medication categories.

Dialysis method values expressed using LOINC Answer codes (aligned with LOINC answer list LL2102-3 for 70958-4).

Allowed values for donor liver type (Complete, Partial).

Allowed values for donor type (Living, Deceased).

ValueSet of immunosuppressive drug types.

Allowed types for immunosuppressive maintenance records.

ValueSet of instrumental investigation tests conducted.

Allowed intraoperative complications during liver transplantation.

Allowed values for kidney side.

Allowed UCUM units of measurement for lab result values (unit column).

ValueSet of laboratory tests conducted.

ValueSet of post-transplant outcome types.

Allowed values for Observation.method when reporting maximum vs most recent PRA.

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

ValueSet of post-transplant event types.

Allowed antihypertensive drugs for antihypertensive_treatment.

Allowed type(s) for pre-medication records.

Allowed reference genome build names (GRCh38, GRCh37).

Allowed Rh factor values for transplant recipients and donors.

Allowed transplant types.

Allowed types of biliary anastomosis in liver transplant.

Allowed types of visits in the transplant follow-up schedule.

ABO blood groups for transplant recipients and donors.

Tissue types for biological samples (from the bio_sample table).

Categories of relevant concomitant diseases.

Categories of concomitant medications.

Type of liver donation (complete vs partial).

Living vs deceased donor classification.

Types of immunosuppressive drugs used in the transplant setting.

Type of immunosuppressive maintenance record.

Types of instrumental investigation tests conducted.

Intraoperative complications during liver transplantation.

Side of the kidney for nephrectomy / transplant context.

Types of laboratory tests conducted.

Types of clinical outcomes after transplant.

Distinguishes maximum (historical) vs most recent PRA measurements.

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

Types of post-transplant events.

Antihypertensive drugs used as pre-transplant medication.

Type of pre-transplant medication record.

Reference genome build names.

Rh factor for transplant recipients and donors.

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

Types of biliary anastomosis used in liver transplantation.

Type of visit in the transplant follow-up schedule.

Example biological sample used in Visit example.

Example set of clinical variables for a transplant patient.

Example record of a concomitant disease.

Example concomitant episode for a transplant patient.

Example concomitant medication for a concomitant episode.

Example epigenome (methylation array) study record.

Example genomic test / sequencing platform configuration.

Example immunosuppressant drug definition.

Example record of immunosuppressive induction therapy given to a patient.

Example record of maintenance immunosuppressive therapy for a transplant recipient.

Example imaging/instrumental investigation for a transplant patient.

Example creatinine result for a transplant recipient.

Example definition of a lab test (Albumin).

Example lab report grouping a single creatinine result.

Example immune function marker record for a transplant patient.

Example methylomic record for a locus.

Example microbiology panel for a transplant recipient.

Example outcome record for a transplant patient.

Example outcome type: Chronic renal failure after pLTx.

Example of a patient instrumental investigation linked to InstrumentalInvestigation catalogue.

Example post-transplant event type: Episodes of AKI after LTx.

Example of a post-transplant event (e.g., infection episode).

Example record of pre-transplant medications.

Example GRCh38 reference genome used for genomic tests.

Example target region linked to a genomic test.

Example annotation for a variant occurrence.

Example variant occurrence linked to a target region.

ABO group for the transplant donor.

Example HLA class I typing result (A, B, C) for the donor.

Example HLA class II typing result (DP, DQ, DR) for the donor.

Example PRA (%) recorded for the donor (if available).

Rh type for the transplant donor.

Example donor liver graft type.

An example List that links the donor to donor-level Observations.

Example donor dialysis method prior to kidney transplant.

Example date of histological diagnosis.

Example liver diagnosis and diagnosis date.

ABO group for the transplant recipient.

Example HLA class I typing result (A, B, C).

Example HLA class II typing result (DP, DQ, DR).

Rh type for the transplant recipient.

Most recent PRA (%).

Maximum PRA (%).

An example List that links the transplant recipient to their patient-level Observations.

Example renal diagnosis and diagnosis date.

Example transplant instance mapped from the transplant table.

Example Patient instance conforming to Donor.

Example Patient instance conforming to PatientTransplant.

Example visit instance mapped from the visit table.