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)

• get_pathway_compounds: Get all compounds in a pathway
• get_pathway_reactions: Get all reactions in a pathway
• get_compound_reactions: Get all reactions involving a compound
• get_gene_orthologs: Find orthologous genes across organisms
• batch_entry_lookup: Process multiple KEGG entries efficiently

Cross-References & Integration (2 tools)

• convert_identifiers: Convert between KEGG and external database IDs
• find_related_entries: Find related entries across databases

Resource Templates (8 templates)

• kegg://pathway/{pathway_id}: Pathway information
• kegg://gene/{org}:{gene_id}: Gene details
• kegg://compound/{compound_id}: Compound information
• kegg://reaction/{reaction_id}: Reaction details
• kegg://disease/{disease_id}: Disease information
• kegg://drug/{drug_id}: Drug information
• kegg://organism/{org_code}: Organism details
• kegg://search/{database}/{query}: Search results

Installation

1. Clone or download this server to your local machine
2. Install dependencies:

   cd kegg-server
   npm install
   

3. Build the server:

   npm run build
   

Usage Examples

Pathway Analysis

# Search for glycolysis pathways
search_pathways(query="glycolysis")

# Get human glycolysis pathway
get_pathway_info(pathway_id="hsa00010")

# Get genes in human glycolysis pathway
get_pathway_genes(pathway_id="hsa00010")

Gene Research

# Search for insulin genes
search_genes(query="insulin", organism_code="hsa")

# Get detailed information for human insulin gene
get_gene_info(gene_id="hsa:3630", include_sequences=true)

Compound Investigation

# Search for glucose compounds
search_compounds(query="glucose")

# Get glucose compound information
get_compound_info(compound_id="C00031")

# Search by molecular formula
search_compounds(query="C6H12O6", search_type="formula")

Cross-Database Integration

# Convert KEGG gene IDs to NCBI Gene IDs
convert_identifiers(source_db="hsa", target_db="ncbi-geneid")

# Find pathways related to specific genes
find_related_entries(source_db="genes", target_db="pathway", source_entries=["hsa:3630"])

API Coverage

This server implements the core KEGG REST API operations:

• INFO: Database release information
• LIST: Entry lists and organism catalogs
• FIND: Keyword and structure-based searching
• GET: Detailed entry retrieval
• CONV: Identifier conversion between databases
• LINK: Cross-reference discovery

Supported Organisms

The server supports all organisms in KEGG, including:

• Human (hsa): Homo sapiens
• Mouse (mmu): Mus musculus
• Rat (rno): Rattus norvegicus
• E. coli (eco): Escherichia coli
• Yeast (sce): Saccharomyces cerevisiae
• 5000+ other organisms

Data Types

Pathways

• Reference pathways (map)
• Organism-specific pathways
• KEGG Orthology pathways (ko)
• Enzyme classification pathways (ec)

Genes

• Protein-coding genes
• RNA genes
• Pseudogenes
• Gene sequences (amino acid and nucleotide)

Compounds

• Small molecules
• Metabolites
• Chemical structures
• Molecular properties

Error Handling

The server includes comprehensive error handling:

• Input validation for all parameters
• Graceful handling of API timeouts
• Detailed error messages for debugging
• Fallback mechanisms for optional data

Performance Considerations

• Rate Limiting: Respectful API usage with appropriate delays
• Batch Processing: Efficient handling of multiple entries
• Caching: Optional caching for frequently accessed data
• Timeouts: 30-second timeout for API requests

Use Cases

Research Applications

• Systems Biology: Pathway analysis and network reconstruction
• Drug Discovery: Target identification and compound screening
• Comparative Genomics: Cross-species gene analysis
• Metabolomics: Metabolic pathway investigation
• Disease Research: Gene-disease association studies

Educational Applications

• Biochemistry Teaching: Pathway visualization and exploration
• Bioinformatics Training: Database integration exercises
• Molecular Biology: Gene function and regulation studies

Contributing

This server is built using the Model Context Protocol SDK. To contribute:

1. Fork the repository
2. Make your changes
3. Test thoroughly with various KEGG queries
4. Submit a pull request

License

MIT License - see LICENSE file for details.

Support

For issues related to:

• Server functionality: Check the error logs and validate input parameters
• KEGG API: Refer to the official KEGG REST API documentation
• MCP Protocol: Consult the Model Context Protocol documentation

Version History

• v1.0.0: Initial release with comprehensive KEGG API coverage
  • 30 tools covering all major KEGG databases
  • 8 resource templates for dynamic data access
  • Full support for pathways, genes, compounds, reactions, enzymes, diseases, drugs, modules, glycans, and BRITE hierarchies
  • Advanced analysis tools for cross-database integration
  • Batch processing capabilities
  • Robust error handling and input validation

Acknowledgments

• KEGG Database: Kanehisa Laboratories
• Model Context Protocol: Anthropic
• TypeScript and Node.js communities