Human donor schema and standards

This document describes recommended meta-data standards in PanKbase for reporting human donors in studies of pancreas or purified pancreatic islets.

These recommendations are based on standards used by Human Islet Resource Network (HIRN) resources including the Integrated Islet Distribution Program (IIDP) and the Human Pancreas Analysis Program (HPAP), as well as the University of Alberta IsletCore. In addition, these standards consistent with those outlined in: Hart N, Powers A Diabetologia 2018

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 1

The following fields must be included for a valid submission:

• age: Age of the donor in years (numeric value)
• award: Grant associated with the submission (link to Award)
• 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 2

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

• rrid: Research Resource Identifier (format: "RRID ########")
• bmi: Body mass index in kg/m²
• diabetes_status_description: Description of diabetes status
• diabetes_status: Array of diabetes status terms linked to PhenotypeTerm
• ethnicities: Self-reported ethnicity of the donor
• hba1c: HbA1C percentage measurement
• diabetes_status_hba1c: Diabetes status based on adjusted HbA1C levels
• glucose_loweing_therapy: Type of therapy for managing blood glucose levels
• hospital_stay: Total hours of hospitalization
• donation_type: Type of organ donation (DCD, DBD, NDD, MAID)
• cause_of_death: Primary medical condition that led to death
• sex: Self-reported sex of the donor

Tier 3

Diabetes-Related Fields

Several fields capture information specific to diabetes research:

• diabetes_duration: Duration of diabetes in years
• c_peptide: C-Peptide concentration in ng/ml
• family_history_of_diabetes: Boolean indicating family history of diabetes
• family_history_of_diabetes_relationship: Array describing relationship to diabetic family members

Autoantibody Testing

Fields for capturing autoantibody test results:

• aab_gada: Boolean indicating presence of GADA autoantibodies
• aab_gada_value: Numeric value of GADA autoantibodies in unit/ml
• aab_iaa: Boolean indicating presence of IAA autoantibodies
• aab_iaa_value: Numeric value of IAA autoantibodies in unit/ml
• aab_ia2: Boolean indicating presence of IA2 autoantibodies
• aab_ia2_value: Numeric value of IA2 autoantibodies in unit/ml
• aab_znt8: Boolean indicating presence of ZNT8 autoantibodies
• aab_znt8_value: Numeric value of ZNT8 autoantibodies in unit/ml

Demographic and Phenotypic Information

• genetic_ethnicities: Inferred ancestry from genetic analysis
• phenotypic_features: List of associated phenotypic features
• biological_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
• dbxrefs: 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 required fields are completed
• Include as many recommended 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