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omnipath-client

Python client for the OmniPath molecular biology prior-knowledge web API.

omnipath-client provides validated, cache-aware access to the OmniPath API, delivering results as polars, pandas, or pyarrow DataFrames. Network data can optionally be returned as annnet graph objects.

Features

  • Export endpoints for entities, interactions, and associations (complexes, pathways, reactions)
  • Ontology endpoints for term lookup, search, and hierarchy trees
  • Multi-backend DataFrame output: polars (default), pandas, pyarrow
  • Query validation against the API schema (endpoint names, parameter names, enum values)
  • Caching of downloaded data via download-manager
  • Graph conversion to annnet objects for network data

Quick example

import omnipath_client as op

# Get all interactions as a polars DataFrame
df = op.interactions()

# Filter by direction
df = op.interactions(direction='directed')

# Get entities for a specific organism
df = op.entities(taxonomy_ids=['9606'])

# Return interactions as an annnet graph
g = op.interactions(as_graph=True)

Getting started