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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

At the moment, we don't implement any specific configuration options for NetworkX. Feel free to reach out and create issues or pull requests if you need specific configuration options. They would be added to the configuration similarly as for other outputs:

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()