When setting the dbms parameter in the biocypher_config.yaml to csv, the BioCypher Knowledge Graph is written to CSV files.

CSV settings

To overwrite the standard settings of the CSV writer, add a csv section to the biocypher_config.yaml file. The following settings are possible:

  ### CSV/Pandas configuration ###
  delimiter: ','  # The delimiter used in the CSV files. Default is ','.

Offline mode

Running BioCypher

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

  • *.csv: The CSV files containing the node/edge data.

  • import_pandas_csv.csv: A Python script to load the created CSV files into Pandas DataFrames.