Quick Tutorial

Below are some small, fully runnable, code blocks that show how to download, edit, and upload networks in NDEx using CX2 and the new network data model CX2Network

Note

This page was updated with 3.7.0 release of NDEx2 Python client. The Legacy Quick Tutorial can be found here

Download network from NDEx 

The code block below uses the Ndex2 client to download BioGRID: Protein-Protein Interactions (SARS-CoV) network from NDEx as a CX2Network

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

import json
import ndex2
from ndex2.cx2 import RawCX2NetworkFactory, CX2NetworkXFactory

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

# Create CX2Network factory
factory = RawCX2NetworkFactory()

# Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
# https://www.ndexbio.org/viewer/networks/669f30a3-cee6-11ea-aaef-0ac135e8bacf
client_resp = client.get_network_as_cx2_stream('669f30a3-cee6-11ea-aaef-0ac135e8bacf')

# Convert downloaded network to CX2Network object
net_cx = factory.get_cx2network(json.loads(client_resp.content))

# Display information about network and output 1st 100 characters of CX2
print('Name: ' + net_cx.get_name())
print('Number of nodes: ' + str(len(net_cx.get_nodes())))
print('Number of nodes: ' + str(len(net_cx.get_edges())))
print(json.dumps(net_cx.to_cx2(), indent=2)[0:100])

# Create CX2NetworkXFactory
nxfac = CX2NetworkXFactory()
# Create Networkx network
g = nxfac.get_graph(net_cx)

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))

Upload new network to NDEx 

The code block below shows how to upload a network that is a CX2Network to NDEx.

import ndex2
from ndex2.cx2 import CX2Network

# Create a test network
net_cx = CX2Network()

# Set name of network
net_cx.set_name('Upload new network to NDEx')

# Create two nodes and one edge
node_one_id = net_cx.add_node(attributes={'name': 'node 1'})
node_two_id = net_cx.add_node(attributes={'name': 'node 2'})

net_cx.add_edge(source=node_one_id, target=node_two_id, attributes={'interaction': 'link'})

# Create client, be sure to replace <USERNAME> and <PASSWORD> with NDEx username & password
client = ndex2.client.Ndex2(username='<USERNAME>', password='<PASSWORD>')

# Save network to NDEx, value returned is link to raw CX data on server.
res = client.save_new_cx2_network(net_cx.to_cx2(), visibility='PRIVATE')

print(res)
# Example return value:
# https://www.ndexbio.org/v2/network/4027bead-89f2-11ec-b3be-0ac135e8bacf
# To view network in NDEx replace 'v3' with 'viewer' like so:
# https://www.ndexbio.org/viewer/networks/4027bead-89f2-11ec-b3be-0ac135e8bacf

Update network on NDEx 

The code block below shows how to update a network already on NDEx

import json
import io
import ndex2
from ndex2.client import DecimalEncoder
from ndex2.cx2 import RawCX2NetworkFactory, CX2NetworkXFactory

# Create client, be sure to replace <USERNAME> and <PASSWORD> with NDEx username & password
client = ndex2.client.Ndex2(username='<USERNAME>', password='<PASSWORD>')

# Create CX2Network factory
factory = RawCX2NetworkFactory()

# Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
client_resp = client.get_network_as_cx2_stream('<UUID OF NETWORK TO UPDATE>')

# Convert downloaded network to CX2Network object
net_cx = factory.get_cx2network(json.loads(client_resp.content))

# Change networks name
net_attrs = net_cx.get_network_attributes()
if 'name' in net_attrs:
    net_attrs['name'] = 'Updated ' + str(net_attrs['name'])
else:
    net_attrs['name'] = 'Updated network'

# Update network attributes
net_cx.set_network_attributes(net_attrs)

# Create bytes stream
cx_stream = io.BytesIO(json.dumps(net_cx.to_cx2(),
                                  cls=DecimalEncoder).encode('utf-8'))

# Update network in NDEx by completely replacing the network with
# one set in cx_stream
client.update_cx2_network(cx_stream, '<UUID OF NETWORK TO UPDATE>')

# NOTE: above call will not return any output

Add nodes, edges, and attributes to network

The code block below shows how to add nodes, edges and attributes to a CX2Network object

import ndex2
from ndex2.cx2 import CX2Network

# create an empty CX2Network object
# a CX2Network could also be downloaded from NDEx or created from CX2 data
net_cx = ndex2.cx2.CX2Network()

# create a node, id of node is returned, coordinates x and y set below are optional
node_one_id = net_cx.add_node(attributes={'name': 'foo',
                                          'altname': 'alternate name for foo',
                                          'represents': 'representing foo'},
                                          x=10, y=0)

# create another node
node_two_id = net_cx.add_node(attributes={'name': 'bar',
                                          'altname': 'alternate name for bar',
                                          'represents': 'representing bar'},
                                          x=10, y=10)

# create an edge connecting the nodes, id of edge is returned
edge_id = net_cx.add_edge(source=node_one_id, target=node_two_id,
                          attributes={'interaction': 'interacts',
                                      'weight': 0.5})

net_cx.set_network_attributes({'name': 'test network'})

print('Name: ' + net_cx.get_name())
print('Number of nodes: ' + str(len(net_cx.get_nodes())))
print('Number of edges: ' + str(len(net_cx.get_edges())))

Build a lookup table for node names to node ids

The code block below shows how to iterate through nodes in a CX2Network object and build a dict of node names to node ids. The network downloaded below is Multi-Scale Integrated Cell (MuSIC) v1

import json
import ndex2
from ndex2.cx2 import RawCX2NetworkFactory


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

# Download MuSIC network from NDEx
client_resp = client.get_network_as_cx2_stream('7fc70ab6-9fb1-11ea-aaef-0ac135e8bacf')

# Create CX2Network factory
factory = RawCX2NetworkFactory()

# Convert downloaded network to NiceCXNetwork object
net_cx = factory.get_cx2network(json.loads(client_resp.content))

node_name_dict = {}

# Build dictionary and print out all the nodes
for node_id, node_obj in net_cx.get_nodes().items():
    print('node_id: ' + str(node_id) + ' node_obj: ' + str(node_obj))
    node_name_dict[node_obj['v']['name']] = node_id

# Print out dictionary
print(str(node_name_dict))

Quick Tutorial

Download network from NDEx

Upload new network to NDEx

Update network on NDEx