kegg-database

Query KEGG REST API for pathways, gene mappings, and ID conversions.

557|98|Updated Nov 7, 2025
One-click install
npx skills add https://github.com/jimmc414/Kosmos --skill kegg-database-jimmc414
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/kegg-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill kegg-database-jimmc414

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, gene-pathway mappings, metabolic pathways, drug interactions, and perform ID conversions for biological research.

Core Features & Use Cases

  • Pathway Analysis: Retrieve and analyze metabolic pathways, signaling pathways, and disease pathways.
  • Gene/Compound Mapping: Map genes to pathways, compounds to reactions, and vice-versa.
  • ID Conversion: Convert between KEGG IDs and external database identifiers (e.g., UniProt, NCBI Gene).
  • Use Case: A researcher needs to find all human genes associated with the 'Glycolysis' pathway and then retrieve the KEGG pathway map for visualization.

Quick Start

Use the kegg-database skill to find all human pathways associated with 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 using a REST API?

You can query KEGG biological pathways by using Python helper functions that provide direct REST API access to retrieve metabolic, signaling, and disease pathway data programmatically. This Skill handles all REST operations for academic research workflows.

Can I convert KEGG IDs to external database identifiers like NCBI Gene?

Yes, you can convert KEGG IDs to external database identifiers like NCBI Gene and UniProt. The Skill supports identifier conversion to bridge curated biological knowledge across different databases for research.

How do I map human genes to specific metabolic pathways in KEGG?

To map human genes to metabolic pathways, provide a gene identifier like 'hsa:10458' to the Skill. It queries the KEGG API to retrieve all associated pathways, enabling gene-pathway mapping and visualization for biological research.

Does this Skill support checking drug interactions through the KEGG database?

Yes, the Skill supports drug interaction checks by querying the KEGG database. It provides direct REST API access to explore curated drug interaction data alongside metabolic pathway analysis and compound-to-reaction mapping.

What is the best way to integrate KEGG pathway analysis into an automated research workflow?

The best way to integrate KEGG pathway analysis is by using this Skill's Python helper functions to programmatically query the REST API. It enables automated retrieval of pathway maps, gene mappings, and ID conversions without manual database searches.

Are there limitations when using the KEGG REST API for pathway exploration?

The Skill provides direct REST API access to the KEGG database, meaning results depend on KEGG's curated biological knowledge and API availability. It is designed for academic research workflows rather than real-time clinical data processing.