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bioservices

Access 40+ bioinformatics services and databases via a unified Python API.

16|7|Updated Nov 20, 2025
Search Tags:#bioinformatics#KEGG#UniProt#identifier mapping#bioservices#PPI
One-click install
npx skills add https://github.com/jackspace/ClaudeSkillz --skill bioservices
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-pkg-bioservices
Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill bioservices

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires bioservices, and includes references (resource) components.

What problem does it solve?

BioServices provides programmatic access to approximately 40 bioinformatics web services and databases from Python, enabling automated data retrieval, cross-database queries, and identifier mappings for reproducible research.

Core Features & Use Cases

  • Protein Analysis: search UniProt, retrieve sequences, map identifiers
  • Pathway Discovery and Analysis: KEGG, Reactome, and GO queries
  • Compound Database Searches: cross-reference KEGG, ChEBI, ChEMBL mappings
  • Sequence Analysis: BLAST-like workflows and sequence retrieval
  • Multi-Service Workflows: integrate data from multiple services into Python pipelines
  • Protein-Protein Interactions: access PSICQUIC-compatible resources

Quick Start

Install bioservices and run a quick UniProt search:

  1. Install: pip install bioservices
  2. Example (no shell fences): from bioservices import UniProt u = UniProt() results = u.search("ZAP70_HUMAN", frmt="tab", columns="id,genes,organism") print(results)

Frequently Asked Questions about bioservices

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query multiple bioinformatics databases from Python without learning each API?▼

Bioservices provides a unified Python API for 40+ bioinformatics services including UniProt, KEGG, ChEMBL, and PubChem, letting you retrieve proteins, sequences, pathways, and compounds through consistent method calls instead of separate database protocols.

Can I map identifiers across UniProt, KEGG, and other databases in a single workflow?▼

Yes. Bioservices handles identifier mapping across multiple databases, enabling you to cross-reference protein IDs, genes, and compounds and integrate results into reproducible Python pipelines without manual format conversion.

How do I retrieve protein sequences and pathway information from REST and SOAP services?▼

Bioservices abstracts both REST and SOAP/WSDL protocols, so you call the same Python methods to fetch protein data from UniProt, pathway data from Reactome or KEGG, and GO terms, with the library handling protocol differences internally.

What's the best way to automate protein-protein interaction and compound database searches?▼

Bioservices integrates PSICQUIC-compatible resources and compound databases like ChEBI and ChEMBL into Python workflows, letting you automate multi-service queries and cross-reference interactions without switching tools or writing custom API wrappers.

Do I need to write separate code for each bioinformatics database service?▼

No. Bioservices consolidates ~40 services into one library with consistent syntax for UniProt searches, KEGG queries, sequence retrieval, and compound lookups, reducing code duplication and maintenance overhead in research pipelines.

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