Ukb Navigator

Data Sources

Workflow

When the user asks about UK Biobank data:

1. Embed (first use): Index UKB schema into ChromaDB with Voyage AI embeddings
2. Search: Semantic search against the embedded schema
3. Rank: Return top matches by cosine similarity
4. Report: Generate markdown report with field IDs, descriptions, and relevance scores

Example Queries

• "What UK Biobank fields measure kidney function?"
• "Find all imaging-derived brain phenotypes"
• "Look up UKB field 21001"
• "Which fields capture medication use?"
• "Blood biomarkers related to inflammation"

Output Structure

output_directory/
├── report.md                    # Full markdown report with matched fields
├── matched_fields.csv           # Structured table of matching fields
└── reproducibility/
    └── commands.sh              # CLI command to reproduce this search

Demo Mode

Run --demo to search using pre-cached schema results without requiring UKB data files:

python ukb_navigator.py --demo --output /tmp/ukb_demo

The demo searches for "blood pressure and hypertension" and returns sample field matches.

Dependencies

Required:

• chromadb >= 0.4 (vector database)
• Python 3.10+

Optional:

• voyageai (Voyage AI embeddings — falls back to ChromaDB default if absent)

Safety

• All processing is local — no data leaves this machine
• UK Biobank schema is publicly available metadata (not patient data)
• No individual-level UKB data is included or transmitted
• Requires valid UKB data access application for actual research use

Integration with Bio Orchestrator

This skill is invoked by the Bio Orchestrator when:

• User mentions "UK Biobank", "UKB", "Biobank fields", "UKB schema"
• User asks about finding variables or fields in a large biobank
• Query contains keywords: "ukb", "uk biobank", "biobank navigator"

It can be chained with:

• gwas-prs: Use discovered field IDs to define phenotypes for PRS analysis
• gwas-lookup: Look up GWAS associations for variants in UKB-identified phenotypes
• lit-synthesizer: Find publications about UKB-derived phenotypes