When setting the dbms parameter in the biocypher_config.yaml to networkx, the BioCypher Knowledge Graph is transformed into a NetworkX DiGraph and then written to a pickle file.

NetworkX settings

To overwrite the standard settings of NetworkX, add a networkx section to the biocypher_config.yaml file. At the moment there are no configuration options supported/implemented. Feel free to reach out and create issues or pull requests if you need specific configuration options.

  ### NetworkX configuration ###

Offline mode

Running BioCypher

After running BioCypher with the offline parameter set to true and the dbms set to networkx, the output folder contains:

  • networkx_graph.pkl: The pickle file containing with the BioCypher Knowledge Graph as NetworkX DiGraph.

  • A Python script to load the created pickle file.


If any of the files is missing make sure to run bc.write_import_call().