ariadnepy 0.1.0

Python interface to the ariadne multi-omic knowledge graph

ariadnePy

Python interface to the ariadne multi-omic knowledge graph.

ariadnePy brings the biological database integration and graph-theory tools of the R package ariadne to Python users. It downloads biological resources (Gene Ontology, KEGG, UniProt, BugSigDB, ChocoPhlAn, and more) from Zenodo and assembles them into a single NetworkX MultiDiGraph that can be queried, filtered, and visualised directly in Python.

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Installation

pip install ariadnepy

To also read RDS files (required for MSigDB):

pip install "ariadnepy[rds]"

For development:

git clone https://github.com/Minotau-R/ariadnePy
cd ariadnePy
pip install -e ".[dev]"

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Quick start

import ariadnepy

# Build the knowledge graph using default resource versions
# (downloads GML files from Zenodo on first run; cached locally afterwards)
g = ariadnepy.ariadne()

print(g)
# MultiDiGraph with N nodes and M edges

# List all available resource versions
df = ariadnepy.list_resource_versions()
print(df.head())

# Select specific versions
g = ariadnepy.ariadne(versions={"GO": "2026-01-23", "KEGG": "latest"})

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Project structure

ariadnePy/
├── src/
│   └── ariadnepy/
│       ├── __init__.py     # public API
│       ├── _core.py        # ariadne() graph builder
│       ├── _cache.py       # resource downloading & caching
│       ├── _utils.py       # utility functions
│       └── _custom.py      # custom resource support
├── tests/
│   ├── test_core.py
│   ├── test_cache.py
│   └── test_utils.py
├── pyproject.toml
└── README.md

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Running tests

pytest

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License