![Logo](logo.png) # 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](https://augmentednature.ai)** ## 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: ```bash cd kegg-server npm install ``` 3. Build the server: ```bash 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