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omnipath-client

The easiest way to access molecular biology knowledge in Python.

omnipath-client connects you to the OmniPath ecosystem -- a comprehensive collection of molecular biology databases covering signaling, gene regulation, protein interactions, metabolomics, and more.

Why OmniPath?

OmniPath integrates data from 200+ databases into a unified resource: protein-protein interactions, enzyme-substrate relationships, transcription factor targets, protein complexes, functional annotations, intercellular communication, and metabolite networks. Instead of querying dozens of databases individually, query OmniPath once.

Why this client?

  • No setup needed -- queries the web service, no local database required
  • 97 identifier types -- translate between UniProt, gene symbols, Ensembl, ChEBI, HMDB, and 90+ other ID systems
  • 28,000 organisms -- taxonomy resolution across NCBI, Ensembl, KEGG, OMA
  • Orthology -- cross-species gene translation with 6 backends
  • DataFrames -- returns polars, pandas, or pyarrow DataFrames
  • BSD-3-Clause -- free to use in any project

Quick examples

Translate gene symbols to UniProt

from omnipath_client.utils import map_name, translation_df

map_name('TP53', 'genesymbol', 'uniprot')
# {'P04637'}

# Full translation table as DataFrame
df = translation_df('genesymbol', 'uniprot')

Cross-species translation

from omnipath_client.utils import orthology_translate

orthology_translate(['TP53', 'EGFR'], source=9606, target=10090)
# {'TP53': {'Trp53'}, 'EGFR': {'Egfr'}}

Query protein interactions

import omnipath_client as op

# One-call helper: caffeine drug targets with UniProt + gene symbols
op.related(
    'caffeine',
    sources=['bindingdb'],
    id_types=['name', 'uniprot', 'genesymbol'],
)

# Or the lower-level primitive
df = op.relations(entity_pks=['2119890'])

Resolve and enrich identifiers

op.lookup(
    ['caffeine', 'metformin', 'TP53'],
    id_types=['name', 'chebi', 'hmdb', 'uniprot', 'genesymbol'],
)

Explore the API

import omnipath_client as op

op.endpoints()                                       # all endpoints
op.params('exports/relations/parquet')                # available filters
op.values('exports/entities/parquet', 'entity_types') # allowed values
op.resources()                                        # source catalog

Learn more

Services

Service URL What it provides
OmniPath Database dev.omnipathdb.org Interactions, annotations, complexes, ontology
OmniPath Utils utils.omnipathdb.org ID translation, taxonomy, orthology, reference lists
OmniPath Metabo metabo.omnipathdb.org COSMOS PKN, metabolite-protein interactions