phenopacket-ingest

Koza ingest for phenopacket data, transforming phenopackets from the phenopacket-store into Biolink model format for knowledge graph integration.

Data Source

Phenopacket Store contains structured phenotypic data about rare disease cases in the GA4GH Phenopacket format.

Data is downloaded from: https://github.com/monarch-initiative/phenopacket-store/releases/latest/download/all_phenopackets.zip

Output

This ingest produces:

• Case nodes - Individual cases with subject information
• Case-to-phenotype associations - Links cases to phenotypic features (HPO terms)
• Case-to-disease associations - Links cases to diseases (MONDO terms)
• Case-to-gene associations - Links cases to genes from interpretation data

Entity ID Format

Case entities use IDs that include the cohort for proper URI resolution:

phenopacket.store:{cohort}.{phenopacket_id}

Usage

# Install dependencies
just install

# Run full pipeline
just run

# Or run steps individually
just download      # Download phenopacket data
just preprocess    # Extract to JSONL
just transform-all # Run Koza transform
just test          # Run tests

Requirements

• Python 3.10+
• uv package manager
• just command runner

License

BSD-3-Clause