kegg-database

Query KEGG REST API for pathways, genes, compounds, and ID conversion.

Updated Mar 10, 2026

Search Tags:#bioinformatics #pathway analysis #gene mapping #drug interactions #kegg #id conversion

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill kegg-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/kegg-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill kegg-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides direct access to the KEGG database, enabling users to query biological pathways, genes, compounds, and drug interactions programmatically.

Core Features & Use Cases

Pathway Analysis: Retrieve detailed information about metabolic, genetic, and cellular pathways.
ID Conversion: Map identifiers between KEGG and external databases like UniProt and NCBI.
Drug Interaction Data: Check for potential drug-drug interactions.
Use Case: A researcher needs to find all human genes associated with the 'Glycolysis' pathway and then retrieve their corresponding UniProt IDs for further analysis.

Quick Start

Use the kegg-database skill to find all human pathways linked to the gene 'hsa:10458'.

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 biological pathways for gene mapping programmatically?▼

You can query KEGG biological pathways for gene mapping programmatically by using this Skill's Python helper functions to access the KEGG REST API, retrieving detailed metabolic and genetic pathway information directly.

Can I convert KEGG gene identifiers to UniProt or NCBI IDs for academic research?▼

Yes, you can convert KEGG gene identifiers to UniProt or NCBI IDs by utilizing the Skill's ID conversion features, which map identifiers between the KEGG database and external biological databases for academic research workflows.

How do I retrieve compound and drug interaction data from the KEGG database?▼

To retrieve compound and drug interaction data from the KEGG database, the Skill provides direct REST API access to query molecular interactions, enabling you to check for potential drug-drug interactions programmatically.

Does this KEGG API integration require installing external Python dependencies?▼

No, this KEGG API integration does not require installing external Python dependencies, as the Skill operates independently with built-in Python helper functions to execute all KEGG REST API operations for pathway analysis.

What is the best way to find all human genes associated with a specific metabolic pathway like Glycolysis?▼

The best way to find all human genes associated with a metabolic pathway like Glycolysis is using this Skill to query the KEGG REST API, which retrieves all linked human genes and their corresponding external database IDs.

Are there limitations when accessing KEGG pathway analysis via REST API for large-scale batch queries?▼

This Skill provides direct REST API access for KEGG pathway analysis, meaning limitations are bound by standard KEGG API rate limits and query constraints, making it best suited for targeted academic research workflows rather than massive batch retrieval.