PanKbase — Human donor schema and standards

This document outlines the recommended metadata standards in PanKbase for reporting human organ donors in studies involving the pancreas and/or purified pancreatic islets.

These recommendations are based on standards developed by resources including the Integrated Islet Distribution Program (IIDP), Human Pancreas Analysis Program (HPAP), as well as the University of Alberta IsletCore. In addition, these standards are consistent with those outlined in Hart N & Powers A, Diabetologia 2018, Brissova et al., Diabetes 2019, and Brissova et al., Diabetologia 2019

Schema URL: https://data.pankbase.org/profiles/human_donor/

The Human Donor data model is designed to capture comprehensive information about human donors who contribute biosamples for research, including cell lines.

Tier 0

The following fields are strictly required and must be included for a valid submission:

Age (years): Age of the donor in years (numeric value)
Center Donor ID: Donor center ID identifier for cross-referencing
Lab: Lab associated with the submission (link to Lab)
Living Donor: Boolean indicating if the donor is living
Taxa: Species of the organism (must be "Homo sapiens")

Tier 1

The following fields are required for complete submissions:

Gender: Self-reported gender of the donor
BMI: Body mass index in kg/m²
Description of diabetes status: Indicates the specific type of diabetes or absence of it. It provides more detail than just a yes/no classification. Allowed Values: type 1 diabetes, type 2 diabetes, gestational diabetes, maturity onset diabetes of the young (MODY), monogenic diabetes, neonatal diabetes, wolfram syndrome, Alström syndrome, latent autoimmune diabetes in adults (LADA), type 3c diabetes, steroid-induced diabetes, cystic fibrosis-related diabetes, control without diabetes, diabetes unspecified)

Tier 2

While not strictly required, the following fields are highly recommended for comprehensive data submission:

RRID: Research Resource Identifier
Self-Reported Ethnicity: Self-reported ethnicity of the donor
HbA1C (percentage): HbA1C percentage measurement
Glucose Lowering Therapy: Type of therapy for managing blood glucose levels
Hospital Stay (hours): Total hours of hospitalization
Donation Type: Type of organ donation (Donation after Circulatory Death, Donation after Brain Death, Natural Death Donation, Medical Assistance in Dying)
Cause of Death: Primary medical condition that led to death
Award: Grant associated with the submission (link to Award)

Tier 3

Diabetes-Related Fields

Several fields capture information specific to diabetes research:

Diabetes Duration (years): Duration of diabetes in years
C-Peptide (ng/ml): C-Peptide concentration in ng/ml
Diabetes Status: Ontology Term for diabetes status (MONDO IDs)
Family History of Diabetes: Boolean indicating family history of diabetes
Family History of Diabetes Relationship: Array describing relationship to diabetic family members
T1D stage: At-risk: Single or transient autoantibody, normal glucose level, Stage 1: Two or more autoantibodies, normal glucose metabolism level, Stage 2: Two or more autoantibodies, dysglycemia (e.g., HbA1c ≥ 5.7%), Stage 3: One or more autoantibodies and diagnostic hyperglycemia or T1D diagnosis, Unknown: Insufficient information to determine T1D staging, Unknown: No sufficient information to derive (Reference: Consensus Guidance for Monitoring Individuals With Islet Autoantibodies, ADA Position Statement: Staging Presymptomatic Type 1 Diabetes, TrialNet)
Derived diabetes status: Diabetes is based off A1C value (Normal, Prediabetes, Diabetes)
Other Therapy: Details the type of therapy or medication regimen the patient is on besides glucose lowering therapy

Autoantibody Testing

Fields for capturing autoantibody test results:

AAB GADA POSITIVE: Boolean indicating presence of GADA autoantibodies
AAB GADA assay: Assays used to measure autoantibodies against GADA
AAB GADA value (unit/ml): Numeric value of GADA autoantibodies in unit/ml
AAB IAA POSITIVE: Boolean indicating presence of IAA autoantibodies
AAB IAA assay: Assays used to measure autoantibodies against IAA
AAB IAA value (unit/ml): Numeric value of IAA autoantibodies in unit/ml
AAB IA2 POSITIVE: Boolean indicating presence of IA2 autoantibodies
AAB IA2 assay: Assays used to measure autoantibodies against IA2
AAB IA2 value (unit/ml): Numeric value of IA2 autoantibodies in unit/ml
AAB ZNT8 POSITIVE: Boolean indicating presence of ZNT8 autoantibodies
AAB ZNT8 assay: Assays used to measure autoantibodies against ZNT8
AAB ZNT8 value (unit/ml): Numeric value of ZNT8 autoantibodies in unit/ml

Demographic and Phenotypic Information

Predicted Genetic Ancestry: Inferred ancestry from genetic analysis
Phenotypic Features: List of associated phenotypic features
Genetic Sex: Genetic sex inferred from genomic data

Available Tissues and Data

Pancreas Tissue Available: Boolean indicating if pancreas tissue is available
Other Tissues Available: Array of other available tissues linked to SampleTerm
Data Available: Array of available datasets with tissue and links

Family Relations

Related Donors: Array of familial relations also in PanKbase

Identifiers and References

Accession: Unique identifier (prefixed with PKB, assigned by server)
Aliases: Lab-specific identifiers
External Resources: External resource identifiers
URL: URL for external resource with additional information
Documents: Additional documentation

HLA Typing

HLA typing: Array of HLA typing information as comma-separated values

Submission Guidelines

Ensure all Tier 0 and Tier 1 fields are completed
Include as many Tier 2 and Tier 3 fields as possible for comprehensive data
Use proper formatting for identifiers (RRIDs, accessions, etc.)
Link to appropriate ontology terms for phenotypes and sample types
Follow the pattern requirements for specific fields

Notes for Administrators

Several fields are admin-only and should not be submitted:

Status: Object status (default: "in progress")
Release Timestamp: Date of object release
Schema Version: JSON schema version
UUID: Unique identifier
Collections: Data collections (for DACC use only)
Creation Timestamp: Creation date
Submitted By: User who submitted the object
Notes: DACC internal notes
Human Donor Identifiers: Identifiers of the human donor