PanKbase — Islet biosample 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/primary_islet/

The Primary Islet data model is designed to capture comprehensive information about biosample islet cells that are directly harvested from donors.

Tier 0

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

Cold Ischaemia Time (hours): Duration in hours that the pancreas was kept at a low temperature after removal from the donor
Donor ID: Donor(s) the sample was derived from
Islet Isolation Center: Islet Isolation Center: Facility or location where the islets were isolated, including islet isolation centers affiliated with the Integrated Islet Distribution Program (IIDP), IsletCore at the University of Alberta (Edmonton), Human Pancreas Analysis Program (HPAP), and Prodo.
Lab: Lab associated with the submission
Sample Terms: Ontology terms identifying the biosample
Biosample Type: Specification of whether biosample represents the original biosample obtained at isolation, or was derived from this biosample

Tier 1

The following fields are highly recommended:

RRID: RRID for biosample
Organ Source: Type of organ donor from which the pancreas or pancreatic tissue was obtained (deceased, living, other classifications, unknown)
Resource: Facility or location where the pancreas was processed (HPAP, IIDP, nPOD, University of Alberta IsletCore )
Pre-Shipment Islet Viability (percentage): Percentage of viable cells in the pancreas preparation
Warm Ischemia Duration / Down Time (hours): Duration in hours that the pancreas was without blood supply at body temperature
Pre-Shipment Islet Purity (Percentage): Percentage of the islet tissue in islet
Hand-Picked: Whether the pancreas or its components were manually selected or processed
Assay used to measure purity: Assay used to measure percentage of the pancreas preparation that consists of the target cells or tissue type (Dithizone(DTZ) etc.)
Pre-Shipment Culture Time (hours): Number of hours the pancreas or isolated islets were cultured before being shipped
Islet Function Available: Whether functional assays or data are available for the isolated pancreatic islets pre- or post-shipping (boolean)

Tier 2

Additional fields that provide valuable context and details about the islet sample:

Islet Characteristics

Islet Yield (IEQ): Total number of Islet Equivalents obtained from the pancreas
Pancreas weight (g): Ratio of Islet Equivalents to the weight of the pancreas
Pancreas Digestion Time (hours): Time taken to enzymatically digest the pancreas tissue
Percentage Trapped (percentage): Percentage of islets that are trapped or non-functional
Islet Morphology: Whether the morphology of the islets has been assessed pre- and/or post-shipment (boolean)
Islet Histology: Whether the histology of the islets has been assessed pre- and/or post-shipment (boolean)
Post-Shipment Islet Purity (%): Islet purity after shipment, for biosamples that have been shipped
Post-Shipment Culture Time (hours): Number of hours the isolated islets were cultured after shipment, for biosamples that have been shipped
Post-Shipment islet viability (%): Percentage of viable islet cells remaining after shipping, for biosamples that have been shipped
Post-Shipment Culture Media: Media used to culture islets after shipment arrival (e.g., UW, CMRL). Reported by islet recipient.
Post-Shipment Culture Temperature: Temperature at which islets were cultured after shipment arrival (e.g., 25ºC, 37ºC). Reported by islet recipient.
Post-Shipment Islet Viability Qualitative: Link to imaging data for qualitative post-shipment viability assessment. See https://iidp.coh.org/LinkClick.aspx?fileticket=nkLcMcZL9GQ%3d&portalid=0
Post-Shipment Islet Viability Quantitative: Quantitative percentage of viable islet cells measured after shipment arrival. See https://www.protocols.io/view/quantitative-assessment-of-islet-viability-upon-ar-bp97mr9n
Pre-Shipment Culture Media: Media used to culture islets before shipment (e.g., UW media, CMRL). Reported by Islet Isolation Center.
Pre-Shipment Culture Temperature: Temperature at which islets were cultured before shipment. Reported by Islet Isolation Center.
Shipping Media: Media used for islet shipment (e.g., UW, CMRL). Reported by Islet Isolation Center.
Shipping Temperature: Temperature at which islets were maintained during shipment (e.g., 4ºC, 25ºC)

Sample Processing

FACS Purification: Links to protocols for FACS purification
Preservation Method: Method by which the tissue was preserved
Date Harvested: The date the sample was harvested, dissected or created

Sample Origin and Demographics

Part of Biosample: Links to a larger biosample from which this sample was taken
Originated From: Links to a biosample that was originated from due to cellular processes
Pooled From: The biosamples this biosample is pooled from
Sorted From: Links to a larger sample from which this sample was obtained through sorting
Sorted From Detail: Detail for sample sorted into fractions

Sample Attributes

Post-mortem Interval (hours): The amount of time elapsed since death
Starting Amount: The initial quantity of samples obtained
Starting Amount Units: The units used to quantify the amount of samples obtained

Identifiers and References

Accession: Unique identifier (prefixed with PKB, assigned by server)
Aliases: Lab-specific identifiers
Lot ID: Lot identifier provided by the originating lab or vendor
Product ID: Product identifier provided by the originating lab or vendor
URL: URL for external resource with additional information
Documents: Additional documentation
Common Coordinate Framework Identifier: HubMap CCF unique identifier
Award: Grant associated with the submission

Modifications and Treatments

Treatments: List of treatments applied to the biosample
Modifications: Links to modifications applied to this biosample
Biomarkers: Biological markers associated with this sample

Construct Library Info

Construct Library Sets: Sets of vectors introduced to this sample
Multiplicity Of Infection: The actual MOI for vectors introduced to this sample
Nucleic Acid Delivery: Method of introduction of nucleic acid into the cell
Time Post Library Delivery: Time elapsed after construct library introduction
Time Post Library Delivery Units: Units for time post library delivery
Cellular Sub Pool: Cellular sub-pool fraction of the sample
Protocols: Links to protocols for preparing the samples

Submission Guidelines

Ensure all Tier 0 fields are completed
Include as many Tier 1 fields as possible for comprehensive data
Add relevant Tier 2 fields for complete sample characterization
Use proper formatting for identifiers and dates
Link to appropriate ontology terms for sample types and disease terms
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
External Resources: Biosample identifiers from external resources
Taxa: The species of the organism (auto-populated based on donor)
Sex: Gender information (auto-populated from donor)
Age: Age of organism at collection time (auto-populated)

The following fields are automatically generated and not submittable:

ID: Object identifier
Type: Object type
Summary: Object summary
File Sets: File sets linked to the sample
Multiplexed In: Multiplexed samples in which this sample is included
Sorted Fraction Samples: Fractions into which this sample has been sorted
Origin Sample Of: Samples which originate from this sample
Institutional Certificates: Institutional certificates for sample approval
Biosample Parts: Parts into which this sample has been divided
Pooled In: Pooled samples in which this sample is included
Classifications: General category of this type of sample