OmniPath (indra.sources.omnipath)

The OmniPath module accesses biomolecular interaction data from various curated databases using the OmniPath API (see and processes the returned data into statements using the OmniPathProcessor.

Currently, the following data is collected:

To process all statements, use the function process_from_web:

>>> from indra.sources.omnipath import process_from_web
>>> omnipath_processor = process_from_web()
>>> stmts = omnipath_processor.statements

OmniPath API (indra.sources.omnipath.api)


Query the OmniPath web API and return an OmniPathProcessor.

Returns:An OmniPathProcessor object which contains a list of extracted INDRA Statements in its statements attribute.
Return type:OmniPathProcessor

OmniPath Processor (indra.sources.omnipath.processor)

class indra.sources.omnipath.processor.OmniPathProcessor(ptm_json=None, ligrec_json=None)[source]

Class to process OmniPath JSON into INDRA Statements.


Process ligand-receptor json if present


Process ptm json if present