Cytoscape networks (indra.assemblers.cx_assembler)

class indra.assemblers.cx_assembler.CxAssembler(stmts=None, network_name='indra_assembled')[source]

This class assembles a CX network from a set of INDRA Statements.

The CX format is an aspect oriented data mode for networks. The format is defined at http://www.home.ndexbio.org/data-model/. The CX format is the standard for NDEx and is compatible with CytoScape via the CyNDEx plugin.

Parameters:
  • stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be assembled.
  • network_name (Optional[str]) – The name of the network to be assembled. Default: indra_assembled
statements

list[indra.statements.Statement] – A list of INDRA Statements to be assembled.

network_name

str – The name of the network to be assembled.

cx

dict – The structure of the CX network that is assembled.

add_statements(stmts)[source]

Add INDRA Statements to the assembler’s list of statements.

Parameters:stmts (list[indra.statements.Statement]) – A list of indra.statements.Statement to be added to the statement list of the assembler.
make_model(add_indra_json=True)[source]

Assemble the CX network from the collected INDRA Statements.

This method assembles a CX network from the set of INDRA Statements. The assembled network is set as the assembler’s cx argument.

Parameters:add_indra_json (Optional[bool]) – If True, the INDRA Statement JSON annotation is added to each edge in the network. Default: True
Returns:cx_str – The json serialized CX model.
Return type:str
print_cx(pretty=True)[source]

Return the assembled CX network as a json string.

Parameters:pretty (bool) – If True, the CX string is formatted with indentation (for human viewing) otherwise no indentation is used.
Returns:json_str – A json formatted string representation of the CX network.
Return type:str
save_model(file_name='model.cx')[source]

Save the assembled CX network in a file.

Parameters:file_name (Optional[str]) – The name of the file to save the CX network to. Default: model.cx
set_context(cell_type)[source]

Set protein expression data and mutational status as node attribute

This method uses indra.databases.context_client to get protein expression levels and mutational status for a given cell type and set a node attribute for proteins accordingly.

Parameters:cell_type (str) – Cell type name for which expression levels are queried. The cell type name follows the CCLE database conventions. Example: LOXIMVI_SKIN, BT20_BREAST
upload_model(ndex_cred)[source]

Creates a new NDEx network of the assembled CX model.

To upload the assembled CX model to NDEx, you need to have a registered account on NDEx (http://ndexbio.org/) and have the ndex python package installed. The uploaded network is private by default.

Parameters:ndex_cred (dict) – A dictionary with the following entries: ‘user’: NDEx user name ‘password’: NDEx password
Returns:network_id – The UUID of the NDEx network that was created by uploading the assembled CX model.
Return type:str