skills.rest
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kegg-database

Query KEGG REST API for pathways, gene mappings, and ID conversions.

1|Updated Jan 14, 2026
Search Tags:#bioinformatics#pathway analysis#gene mapping#drug interactions#kegg#metabolic pathways
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill kegg-database-sologa
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/kegg-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill kegg-database-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides direct access to the KEGG database, enabling users to query biological pathways, gene-pathway mappings, metabolic pathways, drug interactions, and perform ID conversions for academic research.

Core Features & Use Cases

  • Pathway Analysis: Retrieve detailed information about metabolic, genetic, cellular, and disease pathways.
  • Gene-Pathway Mapping: Find which pathways are associated with specific genes or sets of genes.
  • ID Conversion: Translate gene, compound, or drug IDs between KEGG and external databases like UniProt or PubChem.
  • Use Case: A researcher wants to understand the metabolic pathways involved in a specific disease. They can use this Skill to find relevant pathways in KEGG, identify key genes and compounds within those pathways, and map them to known drug targets.

Quick Start

Use the kegg-database skill to find all human pathways associated with the gene TP53.

Frequently Asked Questions about kegg-database

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

FAQPage Schema
How do I map a gene to its associated biological pathways in KEGG?▼

Gene-pathway mapping in KEGG is performed by querying the REST API with a specific gene identifier to retrieve associated metabolic, genetic, cellular, and disease pathway information for academic research.

What is the best way to explore metabolic pathways for drug interaction checks?▼

Exploring metabolic pathways for drug interaction checks involves querying the KEGG REST API to identify key compounds within pathways and map them to known drug interaction targets.

Can I convert gene or compound IDs between KEGG and external databases like UniProt?▼

Yes, ID conversion between KEGG and external databases like UniProt or PubChem is supported. You can translate gene, compound, or drug identifiers using the KEGG REST API operations.

Do I need Python helper scripts to access KEGG biological pathway data?▼

Yes, accessing KEGG biological pathway data through this Skill requires Python helper scripts, which execute all REST API operations for pathway analysis and cross-database integration.

Does KEGG pathway analysis support cross-database integration for academic research?▼

KEGG pathway analysis supports academic research workflows requiring detailed biological network information by providing direct REST API access for cross-database integration and identifier conversion.

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