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bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

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# BioServices

## Overview

BioServices is a Python package providing programmatic access to approximately 40 bioinformatics web services and databases. Retrieve biological data, perform cross-database queries, map identifiers, analyze sequences, and integrate multiple biological resources in Python workflows. The package handles both REST and SOAP/WSDL protocols transparently.

**Version note:** Examples target **bioservices 1.16.0** (PyPI, Mar 2026). Requires **Python 3.9–3.12**. UniProt REST changes in mid-2022 (bioservices ≥1.10) mainly affect tabular `columns` names — see upstream `_legacy_names` if parsing breaks. ChEMBL wrappers changed at 1.6.0 (2018 API); use `get_similarity`, `get_substructure`, `get_molecule` instead of pre-1.6 method names.

## When to Use This Skill

This skill should be used when:
- Retrieving protein sequences, annotations, or structures from UniProt, PDB, Pfam
- Analyzing metabolic pathways and gene functions via KEGG or Reactome
- Searching compound databases (ChEBI, ChEMBL, PubChem) for chemical information