PanKbase Data Library User Guide

The PanKbase Data Library at https://data.pankbase.org is the primary interface for browsing and searching all datasets in PanKbase. This guide walks you through finding, filtering and accessing the data you need.

1. Getting Started

1.1 What You Can Find

1.2 Three Ways to Enter the Library

• Homepage (https://data.pankbase.org) — featured datasets, keyword search, quick links
• Browse Data (https://data.pankbase.org/browse) — choose a data category card
• Direct URL — bookmark searches; filters are preserved in the address bar

2. Data Library Interface Overview

2.1 Homepage

• Search bar: "Search datasets by name, description, or keywords…"
• Featured datasets: some include Download bundles and Browse in library links
• Documentation links: User guide, API, Standards, Schema

2.2 Search List View

• Left panel: facet groups (Donor, Sample, Assay, etc.)
• Object Type: hierarchical list (e.g. Biosample → Primary Islet)
• Center: scrollable result list
• Top right: items per page (25 / 100 / 300); List vs Report view toggle
• Above results: active filter tags (click X to remove)

2.3 Report View (/multireport/)

Report view appears when exactly one data type is selected. It shows a sortable table and export options.

• Click column headers to sort (click again for descending)
• Columns button: show or hide fields (also controls TSV export)
• Download metadata as TSV: export visible columns

2.4 Tip: Excluding a Filter Value

To exclude a facet term (negative filter): click and hold a facet checkbox briefly. The filter chip will indicate exclusion. This is useful when you want "everything except" a specific value.

3. Step-by-Step Search Strategies

3.1 Strategy A: Browse by Category

Best for: exploring what is available in each category.

• Go to Browse Data (/browse) or use a homepage link
• Click a category card (e.g. Donor meta-data)
• Use the left facet panel to narrow results
• Click a record ID to open its detail page
• Switch to Report view if you need a table or TSV export

Example: Finding Type 1 Diabetes Donors

• Browse → Donor meta-data (or open /search/?type=HumanDonor)
• Facet Diabetes Status → select Type 1 Diabetes
• Add optional facets: Gender, Ethnicities, autoantibody status
• Click a donor accession (e.g. PKBDO…) for the full profile

3.2 Strategy B: Keyword Search

Best for: finding data by topic, technology, or free text.

• From the homepage, enter search terms and click Search
• Review Site search results grouped by data type
• Use "View all in list" or "View all in report" for a type
• Refine with facets on the search page

Effective Search Terms

• Disease: Type 1 diabetes, autoantibody, beta cell
• Technology: scRNA-seq, single cell, ATAC-seq, proteomics
• Sample: islets, pancreas, HPAP, IIDP
• Analysis: differential expression, peak counts

3.3 Strategy C: Filter-First

Best for: building cohorts that match specific criteria.

• Open a category URL (e.g. /search/?type=PrimaryIslet)
• Apply facets systematically without using the search bar
• Add more facets to refine
• Switch to Report view → select columns → export TSV
• Bookmark the URL to save your filter combination

3.4 Lookup by ID

If you know an accession (e.g. PKBDO7330CDCK), use ID search: /id-search?id=PKBDO7330CDCK — you will be redirected to the record if found.

4. Navigating Each Data Type

4.1 Human Donors

• Search: /search/?type=HumanDonor
• Detail page: /human-donors/{accession}/

On the detail page you will find:

• Clinical dashboard: demographics, diabetes status, HbA1c
• Autoantibody results (GADA, IA-2, ZNT8, IAA)
• Linked biosamples and experimental data

Common Donor Filters (Facets)

4.2 Biosamples (Islet Biosample Meta-data)

• Browse card: Islet biosample meta-data → /search/?type=Biosample
• Narrow with Object Type → Primary Islet for islet-specific data
• Detail routes: /primary-islet/{id}/, /tissues/{uuid}/, and others

Sample detail pages include:

• Quality metrics: viability, purity, islet yield (IEQ)
• Isolation center and processing details
• Parent donor link and experimental history

4.3 Measurement Sets (Experimental Assays)

• Search: /search/?type=MeasurementSet
• Detail: /measurement-sets/{id}/

Detail pages include:

• Assay method and platform
• Source samples and donors
• Data files and sequencing information
• Islet assay details (where applicable)

4.4 Analysis Results (Three Categories)

4.5 Workflows

• Search: /search/?type=Workflow
• Detail: /workflows/{id}/
• Includes: description, source URL, standards page, analysis steps

5. Cross-Reference Navigation

Records are linked across types. Use detail-page links instead of re-searching when possible:

Donor → Samples → Measurement sets → Analysis sets → Files → Workflow

5.1 Research-Focused Examples

Find all T1D donors with single-cell data:

• Filter donors: Diabetes Status = Type 1 Diabetes
• Search measurement sets: assay term = scRNA-seq (or similar)
• Cross-check donor accessions on both result sets

Access processed beta cell expression data:

• Browse → Principal Analysis Results
• Keyword search: beta cell or relevant analysis name
• Open analysis set → download files from file table

6. Data Export and Access

6.1 External Links

• RRID connections to external databases
• Publication DOIs where available
• GEO/SRA links for raw data in public repositories

7. Quick Reference — URLs

8. Support

• Email: help@pankbase.org
• In-app help: User guide, Standards, and Schema links on the homepage