koza 2.5.0

Data transformation framework for LinkML data models

Koza - Knowledge Graph Transformation and Operations Toolkit

Documentation

Disclaimer: Koza is in beta - we are looking for testers!

Overview

Koza is a Python library and CLI tool for transforming biomedical data and performing graph operations on Knowledge Graph Exchange (KGX) files. It provides two main capabilities:

📊 Graph Operations (New!)

Powerful DuckDB-based operations for KGX knowledge graphs:

• Join multiple KGX files with schema harmonization
• Split files by field values with format conversion
• Prune dangling edges and handle singleton nodes
• Append new data to existing databases with schema evolution
• Multi-format support for TSV, JSONL, and Parquet files

🔄 Data Transformation (Core)

Transform biomedical data sources into KGX format:

• Transform csv, json, yaml, jsonl, and xml to target formats
• Output in KGX format
• Write data transforms in semi-declarative Python
• Configure source files, columns/properties, and metadata in YAML
• Create mapping files and translation tables between vocabularies

Installation

Koza is available on PyPi and can be installed via pip/pipx:

[pip|pipx] install koza

Usage

Quick Start with Graph Operations

Koza's graph operations work seamlessly across multiple KGX formats (TSV, JSONL, Parquet):

# Join multiple KGX files into a unified database
koza join --nodes genes.tsv pathways.jsonl --edges interactions.parquet --output merged_graph.duckdb

# Prune dangling edges and handle singleton nodes
koza prune --database merged_graph.duckdb --keep-singletons

# Append new data to existing database with schema evolution
koza append --database merged_graph.duckdb --nodes new_genes.tsv --edges new_interactions.jsonl

# Split database by source with format conversion
koza split --database merged_graph.duckdb --split-on provided_by --output-format parquet

NOTE: As of version 0.2.0, there is a new method for getting your ingest's KozaApp instance. Please see the updated documentation for details.

See the Koza documentation for complete usage information

Examples

Validate

Give Koza a local or remote csv file, and get some basic information (headers, number of rows)

koza validate \
  --file https://raw.githubusercontent.com/monarch-initiative/koza/main/examples/data/string.tsv \
  --delimiter ' '

Sending a json or jsonl formatted file will confirm if the file is valid json or jsonl

koza validate \
  --file ./examples/data/ZFIN_PHENOTYPE_0.jsonl.gz \
  --format jsonl

koza validate \
  --file ./examples/data/ddpheno.json.gz \
  --format json

Transform

Run the example ingest, "string/protein-links-detailed"

koza transform \
  --source examples/string/protein-links-detailed.yaml \
  --global-table examples/translation_table.yaml

koza transform \
  --source examples/string-declarative/protein-links-detailed.yaml \
  --global-table examples/translation_table.yaml

Note: Koza expects a directory structure as described in the above example
with the source config file and transform code in the same directory:

.
├── ...
│   ├── your_source
│   │   ├── your_ingest.yaml
│   │   └── your_ingest.py
│   └── some_translation_table.yaml
└── ...

Graph Operations

Create and manipulate knowledge graphs from existing KGX files:

# Join heterogeneous KGX files with automatic schema harmonization
koza join \
  --nodes genes.tsv proteins.jsonl pathways.parquet \
  --edges gene_protein.tsv protein_pathway.jsonl \
  --output unified_graph.duckdb \
  --schema-report

# Clean up graph integrity issues
koza prune \
  --database unified_graph.duckdb \
  --keep-singletons \
  --dry-run  # Preview changes before applying

# Incrementally add new data with schema evolution
koza append \
  --database unified_graph.duckdb \
  --nodes new_genes.tsv updated_pathways.jsonl \
  --deduplicate \
  --show-progress

# Export subsets with format conversion
koza split \
  --database unified_graph.duckdb \
  --split-on provided_by \
  --output-format parquet \
  --output-dir ./split_graphs

Key Features

🔧 Multi-Format Support

• Native support for TSV, JSONL, and Parquet KGX files
• Automatic format detection and conversion
• Mixed-format operations in single commands

🛡️ Schema Flexibility

• Automatic schema harmonization across heterogeneous files
• Schema evolution with backward compatibility
• Comprehensive schema reporting and validation

⚡ High Performance

• DuckDB-powered operations for fast bulk processing
• Memory-efficient handling of large knowledge graphs
• Parallel processing and streaming where possible

🔍 Rich CLI Experience

• Progress indicators for long-running operations
• Detailed statistics and operation summaries
• Dry-run modes for safe operation preview

🧹 Data Integrity

• Dangling edge detection and preservation
• Duplicate detection and removal strategies
• Non-destructive operations with data archiving