Tabular output

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()