Unofficial KEGG MCP Server

A Model Context Protocol (MCP) server that provides comprehensive access to the KEGG (Kyoto Encyclopedia of Genes and Genomes) database through its REST API.

Developed by Augmented Nature

Overview

This MCP server enables seamless integration with KEGG’s extensive biological databases, providing tools for pathway analysis, gene research, compound investigation, and cross-database linking. It’s designed for researchers in bioinformatics, systems biology, drug discovery, and related fields.

Features

Database Coverage

• Pathways: KEGG pathway maps and organism-specific pathways
• Genes: Gene information across 5000+ organisms
• Compounds: Chemical compounds and their properties
• Reactions: Biochemical reactions and enzymes
• Diseases: Human diseases and associated genes
• Drugs: Drug information and interactions
• Cross-references: Links between KEGG and external databases

Tool Categories

Database Information & Statistics (2 tools)

• get_database_info: Get release information and statistics
• list_organisms: Get all KEGG organisms with codes and names

Pathway Analysis (3 tools)

• search_pathways: Search pathways by keywords or names
• get_pathway_info: Get detailed pathway information
• get_pathway_genes: Get genes involved in specific pathways

Gene Analysis (2 tools)

• search_genes: Search genes by name, symbol, or keywords
• get_gene_info: Get detailed gene information with optional sequences

Compound Analysis (2 tools)

• search_compounds: Search compounds by name, formula, or structure
• get_compound_info: Get detailed compound information

Reaction & Enzyme Analysis (4 tools)

• search_reactions: Search biochemical reactions by keywords
• get_reaction_info: Get detailed reaction information
• search_enzymes: Search enzymes by EC number or name
• get_enzyme_info: Get detailed enzyme information

Disease & Drug Analysis (5 tools)

• search_diseases: Search human diseases by name or keywords
• get_disease_info: Get detailed disease information
• search_drugs: Search drugs by name, target, or indication
• get_drug_info: Get detailed drug information
• get_drug_interactions: Find adverse drug-drug interactions

Module & Orthology Analysis (4 tools)

• search_modules: Search KEGG modules by name or function
• get_module_info: Get detailed module information
• search_ko_entries: Search KEGG Orthology entries
• get_ko_info: Get detailed KO information

Glycan Analysis (2 tools)

• search_glycans: Search glycan structures by name or composition
• get_glycan_info: Get detailed glycan information

BRITE Hierarchy Analysis (2 tools)

• search_brite: Search BRITE functional hierarchies
• get_brite_info: Get detailed BRITE entry information

Advanced Analysis Tools (4 tools)