NetworkX

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

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.

biocypher_config.yaml

networkx:
  ### 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.

• import_networkx.py: A Python script to load the created pickle file.

Note

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

Online mode

After running BioCypher with the offline parameter set to false and the dbms set to networkx, you can get the in-memory networkx representation of the Knowledge Graph directly from BioCypher by calling the get_kg() function.

# Initialize BioCypher
bc = BioCypher(
    biocypher_config_path="biocypher_config.yaml",
    schema_config_path="schema_config.yaml",
)

# Add nodes and edges
bc.add_nodes(nodes)
bc.add_edges(edges)

# Get the in-memory representation of the Knowledge Graph
in_memory_kg = bc.get_kg()