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bioservices

Cross-reference biological identifiers across UniProt, KEGG, and ChEBI databases.

6|Updated Dec 30, 2025
Search Tags:#bioinformatics#mapping#bioservices#uniprot#pathway#kegg#chebi
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill bioservices-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioservices
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/bioservices
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill bioservices-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Cross-reference biological data across multiple databases and automate cross-database workflows.

Core Features & Use Cases

  • Cross-database identifier mapping (UniProt ↔ KEGG ↔ GO)
  • Pathway discovery and network extraction from KEGG
  • Multi-database compound cross-referencing (ChEBI, ChEMBL via UniChem)
  • Batch processing and error-handling-friendly workflows

Quick Start

Run a minimal script to map a UniProt ID to KEGG and print cross-database identifiers.

Frequently Asked Questions about bioservices

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

FAQPage Schema
How do I cross-reference biological identifiers across UniProt and KEGG?▼

Cross-referencing biological identifiers across UniProt and KEGG is automated through batch mapping scripts that handle protein and gene mappings. The workflows extract cross-database identifiers while managing rate-limiting for reliable bioinformatics analysis pipelines.

What is the best way to automate KEGG pathway discovery in Python?▼

Automating KEGG pathway discovery in Python is handled through bioservices workflows that extract pathway data and network information. These scripts query KEGG directly, enabling pathway extraction and integration into bioinformatics pipelines with built-in error handling.

Can I batch map chemical compounds between ChEBI and ChEMBL?▼

Batch mapping chemical compounds between ChEBI and ChEMBL is supported via UniChem cross-referencing workflows. The skill automates multi-database compound integration, mapping identifiers across these chemical databases with error-handling-friendly workflows designed for bioinformatics processing.

Does the bioservices library support cross-database workflows with GO annotations?▼

The bioservices library supports cross-database workflows including GO annotations by mapping identifiers across UniProt, KEGG, and GO. It integrates these biological databases through Python scripts that handle batch mappings and data integration.

How do I handle rate-limiting when querying multiple bioinformatics databases?▼

Handling rate-limiting when querying multiple bioinformatics databases is built into the cross-database workflows. The scripts incorporate rate-limiting considerations and error handling to ensure stable batch mappings across UniProt, KEGG, ChEBI, and ChEMBL APIs.

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