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kegg-database

Query KEGG REST endpoints for pathway, gene, compound, and drug data.

94|11|Updated Mar 26, 2026
Search Tags:#bioinformatics#rest-api#id-conversion#gene#pathway#kegg
One-click install
npx skills add https://github.com/swaruplab/operon --skill kegg-database-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/kegg-database
Command: npx skills add https://github.com/swaruplab/operon --skill kegg-database-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

KEGG REST API access is essential for pathway analysis, gene-pathway mapping, and cross-database queries, but building robust workflows from scratch can be time-consuming. This Skill provides ready-made Python helpers and reference material to interact with KEGG's REST endpoints, enabling deterministic, reproducible access to pathway, gene, compound, and drug data.

Core Features & Use Cases

  • REST API helpers: Functions to query KEGG info, lists, searches, data retrieval, conversions, links, and drug interactions.
  • Workflow examples: Gene-to-pathway mapping, pathway enrichment context, and cross-database identifier conversions across organisms.
  • Use Case: A researcher quickly fetches human pathway data and maps genes to KO groups for a comparative study.

Quick Start

Query KEGG data for a given gene to retrieve its associated pathways and return a concise summary.

Frequently Asked Questions about kegg-database

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

FAQPage Schema
How do I map genes to pathways using the KEGG REST API?▼

You can map genes to pathways using the KEGG REST API by executing the link operation through the included Python helper, which connects gene identifiers directly to their associated pathway entries.

What is the best way to convert gene identifiers across databases with KEGG?▼

The best way to convert gene identifiers across databases with KEGG is to use the conv REST operation, which translates external database IDs into KEGG identifiers to enable cross-database queries and mapping.

Can I retrieve compound and drug data directly from KEGG?▼

Yes, you can retrieve compound and drug data directly from KEGG by using the get and ddi operations in the Python helper to fetch specific database entries and check drug interactions.

Does this Skill support searching for specific pathways or genes in KEGG?▼

Yes, this Skill supports searching for specific pathways or genes in KEGG by utilizing the find operation, which queries the REST API to locate entries matching your search terms across available databases.

What KEGG REST operations are available for pathway enrichment context?▼

Available KEGG REST operations for pathway enrichment context include info, list, find, get, conv, link, and ddi, allowing you to retrieve, map, and cross-reference pathway, gene, and compound data.

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