omnipath-utils

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