kegg-database

Query KEGG REST data for pathways, genes, compounds, and drugs.

1|Updated Mar 4, 2026

Search Tags:#bioinformatics #conversion #rest-api #drug #gene #pathway #kegg

Ready to run

npx skills add https://github.com/Hung-3008/agusta --skill kegg-database-hung-3008

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/kegg-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill kegg-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Enables researchers to perform direct, programmatic access to KEGG data via REST endpoints for retrieval of pathways, genes, compounds, and drugs without manual web scraping.

Core Features & Use Cases

Provides Python helpers to query KEGG with kegg_info, kegg_list, kegg_find, kegg_get, kegg_conv, kegg_link, and kegg_ddi for flexible data access.
Supports workflow-level tasks such as pathway retrieval, organism-specific listings, ID conversions, and cross-database mappings in bioinformatics research.
Use case: obtain all human pathways, fetch gene members, and map them to UniProt identifiers for downstream analysis.

Quick Start

Retrieve a KEGG pathway entry and inspect the response to validate API access.

Frequently Asked Questions about kegg-database

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

FAQPage Schema

How do I query KEGG pathways and genes programmatically without manual web scraping?▼

To query KEGG pathways and genes programmatically, this Skill provides direct REST API access via Python helpers like kegg_get and kegg_list, retrieving structured bioinformatics data for academic research workflows.

Can I convert KEGG gene IDs to UniProt identifiers for cross-database mapping?▼

Yes, you can convert KEGG gene IDs to UniProt identifiers for cross-database mapping using the kegg_conv function, which handles ID conversion between KEGG and external databases for downstream analysis.

What is the best way to retrieve all human pathways and fetch their gene members?▼

The best way to retrieve all human pathways and fetch gene members is using kegg_list for organism-specific pathway listings and kegg_link to map pathway entries to their associated genes.

How do I find specific compounds and drugs in the KEGG database via REST endpoints?▼

You find specific compounds and drugs in the KEGG database by using the kegg_find function to search entries and kegg_ddi to retrieve drug-drug interaction data directly through the REST API endpoints.

Are there entry limits when fetching bulk pathway or gene data from KEGG REST endpoints?▼

Yes, there are strict entry limits enforced when fetching bulk pathway or gene data from KEGG REST endpoints to manage query sizes and ensure reliable API responses during pathway retrieval and ID conversion.

Do I need any external dependencies to use this KEGG REST API helper?▼

No, you do not need any external dependencies to use this KEGG REST API helper, as it operates independently with internal scripts and references to execute bioinformatics queries for pathways, genes, compounds, and drugs.