README.md

kgsteward - Knowledge Graph Steward

A command line tool to manage the content of RDF store (GraphDB, Fuseki, RDF4J...). Written in python.

Installation

kgsteward is available from PyPI. It depends on hopefully standard Python packages. Its installation should be straightforward.

The recommended option is to install kgsteward with uv

uv tool install kgsteward

or with pip3:

pip3 install kgsteward

You can also clone this repo, and launch kgsteward using the script ./kgsteward at its root

uv run ./kgsteward

Usage

See the documentation

Development

Requirements:

• uv for development.

• Docker installed (we use testcontainers to deploy triplestores for testing)

Run tests, -s will print all outputs:

uv run pytest -s

With HTML coverage report:

uv run pytest -s --cov --cov-report html
python -m http.server 3000 --directory ./htmlcov

Start documentation website in development:

uv run mkdocs serve

References

kgsteward was developed to manage experimental chemical data (LC-MS2) and experimental biological data (bio-activity) data together with reference chemical structures derived from public database (LOTUS, Wikidata) as reported in A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery.