bioservices

SKILL.md

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