bioservices-multi-database

# BioServices Multi-Database Access ## Overview BioServices provides a unified Python interface to 40+ bioinformatics web services including UniProt, KEGG, ChEMBL, ChEBI, PubChem, UniChem, PSICQUIC, QuickGO, and BLAST. Each service is accessed through a consistent object-oriented API with built-in caching, rate limiting, and output format handling. ## When to Use - Querying protein information from UniProt (search, retrieve, ID mapping) - Discovering KEGG pathways and extracting gene/interaction networks - Cross-referencing compounds across ChEMBL, ChEBI, PubChem, and KEGG - Running BLAST sequence similarity searches against UniProtKB - Mapping identifiers between biological databases (UniProt, Ensembl, KEGG, RefSeq, PDB) - Retrieving Gene Ontology annotations via QuickGO - Finding protein-protein interactions via PSICQUIC (IntAct, MINT, BioGRID) - Batch converting thousands of biological identifiers with error handling - For single-database deep queries → use gget (Ensembl), pubchempy (PubChem), or chembl-database-bioactivity skill - For pathway visualization → use pathway analysis tools (Cytoscape, NetworkX) after retrieving data with bioservices ## Prerequisites ```bash pip install bioservices # Optional: pandas for tabular output, matplotlib for visualization pip install pandas matplotlib ``` **API Rate Limits**: Most services have rate limits. bioservices handles basic throttling internally, but for batch operations add explicit delays: - UniProt mapping: ~1 reque...