Individual skill
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
cli-tool/components/skills/scientific/bioservices/SKILL.md
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- Last checked
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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.
## 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)