kgsteward - Knowledge Graph Steward

A command line tool to help manage RDF store (GraphDB). Written in python.

Installation

The code only depends on very standard Python packages. Its installation should be straightforward. The easiest option is to install kgsteward with pip3:

pip3 install git+https://github.com/sib-swiss/kgsteward

# To update your installation to a newer version.
pip3 install --upgrade git+https://github.com/sib-swiss/kgsteward

Alternatively, you can also clone/download the content of this repo to your local machine, and then run kgsteward using the script ./kgsteward.

Important: if the above installation fails or does not build properly (e.g. the package name is set to UNKNOWN), make sure that your versions of pip and setuptools are up-to-date:

pip install --upgrade pip
pip install --upgrade setuptools

Running kgsteward

kgsteward -h

Documentation

The syntax of the YAML configuration file is given here

References

kgsteward was developped 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.