Islet biosample schema and standards

This document describes recommended meta-data standards in PanKbase for reporting pancreatic islet biosamples from human donors

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/primary_islet

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

Tier 1

The following fields must be included for a valid submission:

• award: Grant associated with the submission (link to Award)
• cold_ischaemia_time: Duration in hours that the pancreas was kept at a low temperature after removal
• donors: Donor(s) the sample was derived from (link to Donor)
• isolation_center: Facility where the pancreas was isolated
• lab: Lab associated with the submission (link to Lab)
• sample_terms: Ontology terms identifying the biosample
• sources: The originating lab(s) or vendor(s)

Tier 2

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

• rrid: Research Resource Identifier (format: "RRID ########")
• organ_source: Type of donor from which the pancreas was obtained
• resource: Facility or location where the pancreas was procured
• prep_viability: Percentage of viable cells in the pancreas preparation
• warm_ischaemia_duration: Duration in hours without blood supply at body temperature
• purity: Percentage of the preparation that consists of target cells
• hand_picked: Whether the pancreas components were manually selected
• pre_shipment_culture_time: Hours cultured before shipping
• islet_function_available: Whether functional assays are available

Tier 3

Islet-Specific Fields

Fields specific to islet preparation and quality:

• islet_yield: Total number of Islet Equivalents (IEQ) obtained
• pancreas_weight: Ratio of Islet Equivalents to pancreas weight in grams
• post_shipment_islet_viability: Percentage of viable islet cells after shipping
• percentage_trapped: Percentage of islets that are trapped or non-functional
• digest_time: Time taken to enzymatically digest the pancreas tissue
• islet_morphology: Whether morphology assessment is available
• islet_histology: Whether histology assessment is available

Sample Processing Information

• preservation_method: Method by which the tissue was preserved
• date_obtained: The date the sample was harvested or created
• starting_amount: The initial quantity of samples obtained
• starting_amount_units: Units used to quantify the sample amount
• facs_purification: Links to FACS purification protocols

Sample Relationships

• part_of: Links to a larger biosample from which this was taken
• originated_from: Links to source biosample (for modified samples)
• pooled_from: The biosamples this sample is pooled from
• sorted_from: Links to source sample for sorted fractions
• sorted_from_detail: Details about the sorting process

Biosample Metadata

• lower_bound_age: Lower bound of organism age at collection
• upper_bound_age: Upper bound of organism age at collection
• age_units: Units of time associated with age
• disease_terms: Ontology terms of diseases associated with the sample
• treatments: List of treatments applied to the biosample
• modifications: Links to modifications applied to this biosample
• biomarkers: Biological markers associated with this sample
• embryonic: Whether the biosample is embryonic

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
• protocols: Links to protocols on Protocols.io

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 sample and disease terms
• Include detailed information about the isolation process when available

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 (current: 19)
• 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
• dbxrefs: External resources (admin submission only)

Relationships to Other Data Types

The Primary Islet data model relates to several other data types in the PanKbase database:

• Links to donor information through the donors field
• May be associated with file sets through the file_sets field
• May be part of multiplexed samples through the multiplexed_in field
• May be divided into parts tracked through the parts field
• May be pooled with other samples through the pooled_in field