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:
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.