omnipath-client 0.2.3

The new implementation for the OmniPath Python client

omnipath-client

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

Features

• Export entities, interactions, and associations (complexes, pathways, reactions) as DataFrames
• Ontology term lookup, search, and hierarchy trees
• Multi-backend output: polars (default), pandas, or pyarrow
• Optional graph conversion to annnet objects
• Query validation against the API schema
• Caching via download-manager

Installation

pip install omnipath-client

With polars (recommended default backend):

pip install omnipath-client polars

Quick start

import omnipath_client as op

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

# Directed interactions only
df = op.interactions(direction='directed')

# Human entities
df = op.entities(taxonomy_ids=['9606'])

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

# Ontology term lookup
result = op.ontology_terms(['GO:0006915', 'MI:0326'])

# Choose a different backend
df = op.entities(backend='pandas')

For more examples, see the quickstart guide.

OmniPath Utils

The client provides access to the OmniPath Utils service for ID translation, taxonomy, and orthology:

from omnipath_client.utils import (
    map_name,           # translate identifiers
    translate_column,   # translate DataFrame columns
    ensure_ncbi_tax_id, # resolve organism names
    orthology_translate, # cross-species translation
)

# Gene symbol to UniProt
map_name('TP53', 'genesymbol', 'uniprot')  # {'P04637'}

# Organism resolution
ensure_ncbi_tax_id('mouse')  # 10090

# Cross-species translation
orthology_translate(['TP53'], source=9606, target=10090)
# {'TP53': {'Trp53'}}

Full API: utils.omnipathdb.org

Documentation

Full documentation: saezlab.github.io/omnipath-client

Data licensing

The data served by OmniPath is combined from many original resources, each with their own license terms. The OmniPath client software is BSD-3-Clause, but the data is subject to the licenses of the original sources. Some resources restrict commercial use. Tools and documentation for managing license-based access control will be provided in a future release.

Citation

If you use OmniPath in your research, please cite:

Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D, Doğan T, Domingo-Fernández D, Dugourd A, Gábor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Mañanes D, Módos D, Müller-Dott S, Ölbei M, Schmidt C, Şen B, Theis FJ, Ünlü A, Ulusoy E, Valdeolivas A, Korcsmáros T, Saez-Rodriguez J. (2026) OmniPath: integrated knowledgebase for multi-omics analysis. Nucleic Acids Research 54(D1):D652-D660. doi:10.1093/nar/gkaf1126

License

The client software is licensed under BSD-3-Clause. See Data licensing above for information about the data.