OmniPath (indra.sources.omnipath)

The OmniPath module accesses biomolecular interaction data from various curated databases using the OmniPath API (see https://saezlab.github.io/pypath/html/index.html#webservice) and processes the returned data into statements using the OmniPathProcessor.

Currently, the following data is collected:

• Modifications from the PTMS endpoint https://saezlab.github.io/pypath/html/index.html#enzyme-substrate-interactions

• Ligand-Receptor data from the interactions endpoint https://saezlab.github.io/pypath/html/index.html#interaction-datasets

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)

indra.sources.omnipath.api.process_from_web()

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)

Class to process OmniPath JSON into INDRA Statements.

process_ligrec_interactions()

Process ligand-receptor json if present

process_ptm_mods()

Process ptm json if present