bioservices

# 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 - Converting identifiers between different biological databases (KEGG↔UniProt, compound IDs) - Running sequence similarity searches (BLAST, MUSCLE alignment) - Querying gene ontology terms (QuickGO, GO annotations) - Accessing protein-protein interaction data (PSICQUIC, IntactComplex) - Mining genomic data (BioMart, ArrayExpress, ENA) - Integrating data from multiple bioinformatics resources in a single workflow ## Core Capabilities ###...