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
()[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: OmniPathProcessor