Quick Tutorial

Download network from NDEx

The code blocks below uses the NDEx2 Python client to download BioGRID: Protein-Protein Interactions (SARS-CoV) network from NDEx as a NiceCXNetwork.

The number of nodes and edges are then printed out and the network is converted to Networkx object.

import json
import ndex2

# Create NDEx2 python client
client = ndex2.client.Ndex2()

# Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
# http://ndexbio.org/viewer/networks/669f30a3-cee6-11ea-aaef-0ac135e8bacf
client_resp = client.get_network_as_cx_stream('669f30a3-cee6-11ea-aaef-0ac135e8bacf')

# Convert downloaded network to NiceCXNetwork object
net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(client_resp.content))

# Display information about network and output 1st 100 characters of CX
print('Name: ' + net_cx.get_name())
print('Number of nodes: ' + str(len(list(net_cx.get_nodes()))))
print('Number of nodes: ' + str(len(list(net_cx.get_edges()))))

# Create Networkx network
g = net_cx.to_networkx(mode='default')

print('Name: ' + str(g))
print('Number of nodes: ' + str(g.number_of_nodes()))
print('Number of edges: ' + str(g.number_of_edges()))
print('Network annotations: ' + str(g.graph))

More Tutorials and Examples

To use these tutorials or if Github isn’t showing the above notebooks in the browser, clone the ndex-jupyter-notebooks repository to your local machine and start Jupyter Notebooks in the project directory.

For information on installing and using Jupyter Notebooks, go to jupyter.org