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Tabular Format

When setting the dbms parameter in the biocypher_config.yaml to tabular, csv, or pandas, the BioCypher Knowledge Graph is created in one of several possible tabular formats.

Tabular output 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:

biocypher_config.yaml
csv:
  ### CSV/Pandas configuration ###
  delimiter: ','  # The delimiter to be 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 tabular, csv, or pandas, 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.

Online mode

After running BioCypher with the offline parameter set to false and the dbms set to tabular, csv, or pandas, you can get the in-memory representation of the Knowledge Graph directly from BioCypher by calling the get_kg() function. This returns a dictionary with the corresponding data type (e.g., Pandas dataframes) for every node and edge type.

# 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()