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omnipath-utils

For most users: use omnipath-client

If you just want to translate IDs, resolve organisms, or access reference lists from Python, install the lightweight client instead:

pip install omnipath-client

from omnipath_client.utils import map_name, translate_column
map_name('TP53', 'genesymbol', 'uniprot')  # {'P04637'}

The client queries utils.omnipathdb.org -- no database setup required, same API as the local package.

ID translation, taxonomy, orthology, and reference lists for molecular biology.

omnipath-utils provides a unified API for translating between biological identifiers (UniProt, gene symbols, Ensembl, HGNC, etc.), resolving organism names, and accessing reference lists. It works as a standalone Python library or as an HTTP web service backed by PostgreSQL.

Features

  • ID Translation -- Translate between 97 identifier types across 7+ backends (UniProt, Ensembl BioMart, HMDB, RaMP, etc.)
  • Taxonomy -- Resolve organism names across naming systems (NCBI, Ensembl, KEGG, OMA, miRBase)
  • Reference Lists -- Complete sets of identifiers (all human SwissProt IDs, etc.)
  • Web Service -- Litestar HTTP API with auto-generated OpenAPI schema
  • Database -- PostgreSQL-backed for fast lookups at scale