skills.rest
LogauaEngstrom
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kegg-database

Retrieve KEGG pathway, gene, compound, and drug data via REST API.

18|1|Updated Dec 27, 2025
Search Tags:#bioinformatics#conversion#rest-api#drug#gene#pathway#kegg
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill kegg-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/kegg-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill kegg-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieve KEGG data programmatically via REST API for pathways, genes, compounds, and drugs, eliminating manual web browsing and repetitive queries.

Core Features & Use Cases

  • Python helper functions for KEGG REST operations (info, list, find, get, conv, link, ddi)
  • Comprehensive reference documentation for API usage (kegg_reference.md)
  • Support for batch requests (up to 10 entries), organism-specific queries, and cross-database conversions

Quick Start

Retrieve a glycolysis pathway with hsa00010 using the KEGG REST API.

Frequently Asked Questions about kegg-database

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

FAQPage Schema
How do I retrieve KEGG pathway and gene data programmatically via REST API?▼

Use KEGG REST operations like get, list, and find to programmatically retrieve pathway, gene, compound, and drug data via the REST API, eliminating manual web browsing and repetitive queries.

What is cross-database conversion in KEGG and how does it work?▼

Cross-database conversion uses the KEGG conv operation to map identifiers between databases, enabling bioinformatics workflows to translate gene, compound, and drug entries across different database formats.

Can I batch retrieve multiple KEGG entries in a single REST request?▼

Yes, you can batch retrieve up to 10 KEGG entries per request, allowing efficient data retrieval for multiple genes, compounds, or pathways without triggering individual API calls for each entry.

Does this KEGG REST API access support organism-specific queries?▼

Yes, it supports organism-specific queries across many organisms, allowing you to filter pathway analysis and gene retrieval to specific taxonomic groups using the KEGG REST API.

What are the limitations of using KEGG REST API for academic bioinformatics workflows?▼

It operates under academic-use licensing and supports a maximum of 10 entries per batch request, meaning commercial applications require different licensing and large-scale data extraction needs rate limiting.

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