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 1

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
• Donors 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 a biosample

Tier 2

The following fields are highly recommended for comprehensive data submission:

• 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 tissu
  e 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 3

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
• Post-Shipment islet viability (%): Percentage of viable islet cells remaining after shipping
• 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 shipping
• Post-Shipment Culture Time (hours): Number of hours the isolated islets were cultured after shipping

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
• Virtual: Whether the sample represents a virtual entity rather than physical one

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