domains / families / science / bioservices

bioservices

combined

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). Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping, and integrated biological data workflows with BioServices.

When to use

• 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)

When not to use

• Direct REST control of individual databases

Skill page

Conflict

The three copies overlap on the core BioServices use case (UniProt, KEGG, UniChem, QuickGO, PSICQUIC) but each contains material steps or constraints the others lack. K-Dense-AI provides version-pinned installation, response-type validation, pagination/limit guidance, KEGG rate limits, and SIF namespace caveats. aipoch provides a broader cross-service example including QuickGO and PSICQUIC and optional dependencies. FreedomIntelligence provides BLAST asynchronous workflow, organism/pathway lookup methods, and a direct-REST alternative note. Crowning one would hide real alternatives and constraints.