alterlab-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. ## 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 ### 1. Protein Analysis Retrieve protein information, sequences, and functional annotations: ```python from bioservices import UniProt u = UniProt(verbose=False) # Search for protein by name results = u.search("ZAP70_HUMAN", frmt="tab", columns="id,genes,organism") # Retrieve FASTA sequence sequence = u.retrieve("P43403", "fasta") # Map identifiers between databases kegg_ids =...