OmniPath (indra.sources.omnipath) — INDRA 1.22.0 documentation (original) (raw)
The OmniPath module accesses biomolecular interaction data from various curated databases using the OmniPath API (seehttps://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()[source]
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
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_ligrec_interactions()[source]
Process ligand-receptor json if present
Process ptm json if present