bioservices

Topics in the source

• BioServices
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Protein Analysis
• 2. Pathway Discovery and Analysis
• 3. Compound Database Searches
• 4. Sequence Analysis

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. 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 Retrieve protein information, sequences, and functional annotations: Key methods: search(): Query UniProt with flexible search terms retrieve(): Get protein entries in various format

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