skills.rest
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kegg-database

Query KEGG REST endpoints for pathways, genes, and compounds.

Updated Aug 27, 2026
Search Tags:#bioinformatics#rest api#id-conversion#gene#pathway#data-mapping#kegg
One-click install
npx skills add https://github.com/Org-GAgent/result-interpreter --skill kegg-database-org-gagent
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/Org-GAgent/result-interpreter/tree/main/.skills/scientific-skills/kegg-database
Command: npx skills add https://github.com/Org-GAgent/result-interpreter --skill kegg-database-org-gagent

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Provides direct, programmatic access to KEGG REST endpoints for pathway, gene, and compound data, enabling researchers to fetch information without manual browsing and to build reproducible data pipelines.

Core Features & Use Cases

  • Python helper functions (scripts/kegg_api.py) for KEGG REST API operations (info, list, find, get, conv, link, ddi)
  • Comprehensive reference documentation (references/kegg_reference.md) with API specs, organism codes, and usage guidelines
  • End-to-end workflows for gene-to-pathway mapping, pathway retrieval, and identifier conversions across databases

Quick Start

Query the glycolysis pathway for human (hsa00010) with kegg_get to retrieve full pathway details

Frequently Asked Questions about kegg-database

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

FAQPage Schema
How do I access KEGG pathway data programmatically using Python?▼

You can programmatically access KEGG REST endpoints using Python standard library HTTP capabilities, fetching pathway, gene, and compound data directly. This avoids manual browsing and builds reproducible data pipelines.

What is the best way to map genes to pathways across different organisms in KEGG?▼

The best way to map genes to pathways across organisms is using KEGG REST API link operations. This provides standardized cross-database querying and pathway mapping for reliable data integration across multiple organisms.

Can I convert gene identifiers between KEGG and other databases via REST API?▼

Yes, you can convert identifiers between KEGG and other databases using the KEGG REST API conv operation. This standardizes identifier conversions across databases for cross-database queries and data integration tasks.

Do I need external Python libraries to query KEGG REST endpoints?▼

No, you do not need external libraries to query KEGG REST endpoints. The implementation requires only Python standard library HTTP capabilities, providing a dedicated module to standardize usage without additional dependencies.

How do I retrieve full pathway details like the human glycolysis pathway from KEGG?▼

To retrieve full pathway details like the human glycolysis pathway, use the KEGG REST API get operation with the specific pathway identifier, such as hsa00010. This fetches complete pathway details directly for reproducible analysis.

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