skills.rest
LeonChaoX
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kegg-database

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

783|65|Updated Feb 27, 2026
Search Tags:#pathway analysis#rest api#kegg#id conversion#drug-drug interactions#gene-pathway mapping
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill kegg-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/kegg-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill kegg-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

It solves the problem of manually browsing and downloading KEGG pathway, gene, compound, drug, and interaction data by providing direct programmatic access to KEGG’s REST endpoints.

Core Features & Use Cases

  • KEGG REST API operations via Python helpers: Perform end-to-end retrieval flows (info, list, find, get, convert IDs, link cross-references, and drug-drug interactions) for KEGG-specific workflows.
  • Pathway and molecular data retrieval: Get pathway details in multiple formats (e.g., images, KGML, JSON for single entries; sequences for single genes/proteins; MOL/KCF for compounds).
  • ID conversion and integration: Convert KEGG identifiers to external identifiers (e.g., UniProt, NCBI Gene IDs, PubChem, ChEBI) to connect KEGG outputs with broader bioinformatics pipelines.
  • Use Case: Map a research target (e.g., TP53) to related KEGG pathways, retrieve pathway context, and integrate gene identifiers with external databases for downstream analysis and reporting.

Quick Start

Use the kegg-database skill to retrieve the KEGG entry for pathway ID hsa00010 as standard pathway text.

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 data programmatically for academic analysis?▼

Retrieve KEGG pathway data programmatically by using Python helper functions to query KEGG REST endpoints. You can fetch pathway details in multiple formats like JSON, KGML, or images to support academic pathway analysis and gene-pathway mapping.

Can I convert KEGG gene identifiers to external databases like UniProt or NCBI?▼

Yes, you can convert KEGG gene identifiers to external databases like UniProt, NCBI Gene IDs, PubChem, and ChEBI. The identifier conversion feature connects KEGG outputs with broader bioinformatics pipelines for downstream analysis.

What is the best way to map a specific gene like TP53 to related KEGG pathways?▼

The best way to map a gene like TP53 to KEGG pathways is by using the provided linking and finding helper functions. These tools query KEGG REST endpoints to retrieve pathway context and establish cross-references between genes and pathways.

Does the KEGG REST API support retrieving drug-drug interaction data?▼

Yes, the KEGG REST API supports retrieving drug-drug interaction data. The dedicated helper function queries the KEGG REST endpoints to fetch interaction information for drug-related research and molecular data analysis.

How do I get KEGG compound data in MOL or KCF format?▼

Get KEGG compound data in MOL or KCF format by calling the retrieval helper function with the correct compound ID. This fetches the specific molecular structure data directly from the KEGG REST endpoints for your analysis.

Are there batch-size constraints when fetching KEGG entries via the REST API?▼

Yes, there are batch-size constraints when fetching KEGG entries via the REST API. You must use correct ID formats, output options, and respect batch-size limits provided by the Python helper functions to ensure successful data retrieval.

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