Augmented-Nature/OpenGenes-MCP-Server

Unofficial Open Genes MCP Server

A Model Context Protocol (MCP) server that provides access to the Open Genes API, a comprehensive database of genetic and aging-related data.

Developed by Augmented Nature

Overview

The Open Genes MCP server exposes the Open Genes API functionality through standardized MCP tools, allowing you to query genetic data, aging mechanisms, diseases, and more directly from your MCP-enabled environment.

Features

Gene Search and Retrieval

• search_genes - Search for genes with multiple filter parameters
• get_gene_by_id - Get a specific gene by its ID
• get_gene_by_symbol - Get a gene by its symbol (e.g., "TP53")
• get_gene_by_ncbi_id - Get a gene by its NCBI ID
• get_gene_suggestions - Get gene name suggestions
• get_gene_symbols - Get all available gene symbols
• get_latest_genes - Get recently added genes
• get_genes_by_functional_cluster - Get genes by functional cluster IDs
• get_genes_by_selection_criteria - Get genes by selection criteria IDs
• get_genes_by_go_term - Get genes by GO (Gene Ontology) term
• get_genes_by_expression_change - Get genes by expression change
• get_gene_taxon - Get gene taxon information
• get_genes_increase_lifespan - Get genes that increase lifespan

Taxonomy Tools

• get_model_organisms - Get list of model organisms
• get_phylums - Get list of phylums

Protein Tools

• get_protein_classes - Get protein class information

Disease Tools

• get_diseases - Get disease list
• get_disease_categories - Get disease category list

Research Tools

• get_calorie_experiments - Search calorie restriction experiments
• get_aging_mechanisms - Get aging mechanisms

Installation

The server has been automatically configured in your MCP settings. No additional setup is required.

Usage Examples

Search for genes

Use the search_genes tool with filters:
- byGeneSymbol: "TP53"
- byDiseases: "cancer"
- byAgingMechanism: "cellular senescence"

Get gene information

Use get_gene_by_symbol with:
- symbol: "SIRT1"
- lang: "en"

Get aging mechanisms

Use get_aging_mechanisms with:
- lang: "en"

Language Support

All tools support both English (en) and Russian (ru) languages through the lang parameter.

Pagination

Many tools support pagination through:

• page - Page number (default: 1)
• pageSize - Number of items per page (default: 20)

API Reference

The server connects to the Open Genes API at https://open-genes.com/api

For more information about the Open Genes project, visit: https://open-genes.com

Development

Building

npm run build

Project Structure

open-genes-server/
├── src/
│   ├── index.ts          # Main server implementation
│   ├── tools/            # Tool implementations
│   │   ├── genes.ts      # Gene-related tools
│   │   ├── taxonomy.ts   # Taxonomy tools
│   │   ├── proteins.ts   # Protein tools
│   │   ├── diseases.ts   # Disease tools
│   │   └── research.ts   # Research tools
│   ├── types/            # TypeScript type definitions
│   │   └── api.ts        # API response types
│   └── utils/            # Utility functions
│       └── api-client.ts # Axios instance configuration
├── package.json
├── tsconfig.json
└── README.md

Error Handling

The server includes comprehensive error handling for:

• Network failures
• Invalid parameters
• API errors
• Missing required fields

All errors are returned with descriptive messages to help diagnose issues.