Koza - Knowledge Graph Transformation and Operations Toolkit
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
See the Koza documentation for complete usage information.
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
4 maintainers
Release files for koza 2.6.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| koza-2.6.2.tar.gz | 435.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| koza-2.6.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 603.9 kB
Release files / koza-2.6.2.tar.gz
| Download URL | koza-2.6.2.tar.gz |
|---|---|
| Size | 435.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
uv/0.7.22
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Release files / koza-2.6.2-py3-none-any.whl
| Download URL | koza-2.6.2-py3-none-any.whl |
|---|---|
| Size | 168.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.7.22
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