NDEx CX API (indra.sources.ndex_cx.api)

indra.sources.ndex_cx.api.process_cx(cx_json, summary=None, require_grounding=True)[source]

Process a CX JSON object into Statements.

Parameters

  • cx_json (list) – CX JSON object.

  • summary (Optional[dict]) – The network summary object which can be obtained via get_network_summary through the web service. THis contains metadata such as the owner and the creation time of the network.

  • require_grounding (bool) – Whether network nodes lacking grounding information should be included among the extracted Statements (default is True).

Returns

Processor containing Statements.

Return type

NdexCxProcessor

indra.sources.ndex_cx.api.process_cx_file(file_name, require_grounding=True)[source]

Process a CX JSON file into Statements.

Parameters

  • file_name (str) – Path to file containing CX JSON.

  • require_grounding (bool) – Whether network nodes lacking grounding information should be included among the extracted Statements (default is True).

Returns

Processor containing Statements.

Return type

NdexCxProcessor

indra.sources.ndex_cx.api.process_ndex_network(network_id, username=None, password=None, require_grounding=True)[source]

Process an NDEx network into Statements.

Parameters

  • network_id (str) – NDEx network ID.

  • username (str) – NDEx username.

  • password (str) – NDEx password.

  • require_grounding (bool) – Whether network nodes lacking grounding information should be included among the extracted Statements (default is True).

Returns

Processor containing Statements. Returns None if there if the HTTP status code indicates an unsuccessful request.

Return type

NdexCxProcessor

NDEx CX Processor (indra.sources.ndex_cx.processor)

class indra.sources.ndex_cx.processor.NdexCxProcessor(cx, summary=None, require_grounding=True)[source]

The NdexCxProcessor extracts INDRA Statements from Cytoscape CX JSON.

Parameters

  • cx (list of dicts) – JSON content containing the Cytoscape network in CX format.

  • summary (Optional[dict]) – The network summary object which can be obtained via get_network_summary through the web service. THis contains metadata such as the owner and the creation time of the network.

statements

A list of extracted INDRA Statements. Not all edges in the network may be converted into Statements.

Type

list

get_agents()[source]

Get list of grounded nodes in the network as Agents.

Returns

Only nodes containing sufficient information to be grounded will be contained in this list.

Return type

list of Agents

get_node_names()[source]

Get list of all nodes in the network by name.

get_pmids()[source]

Get list of all PMIDs associated with edges in the network.

get_statements()[source]

Convert network edges into Statements.

Returns

Converted INDRA Statements.

Return type

list of Statements