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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 :py~ndex2.cx.CX2Network

Note

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

Download network from NDEx

The code block below uses the :py~ndex2.client.Ndex2 client to download BioGRID: Protein-Protein Interactions (SARS-CoV) network from NDEx as a :py~ndex2.cx2.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 :py~ndex2.cx2.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 :py~ndex2.cx2.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 :py~ndex2.cx2.CX2Network object and build a :pydict 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))

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