MARRVEL-MCP

<!-- mcp-name: io.github.hyunhwan-bcm/marrvel-mcp -->

A Model Context Protocol (MCP) server for MARRVEL - enabling AI agents to access genetics databases and variant analysis tools for rare disease research.

Demo

Try out MARRVEL-MCP in action:

• <a href="https://chat.marrvel.org">MARRVEL-MCP Chatbot Demo</a>

Quick Start

Installation

git clone https://github.com/hyunhwan-bcm/MARRVEL_MCP.git
cd MARRVEL_MCP

# Using uv (recommended)
uv sync                  # core MCP server only
uv sync --extra eval     # include evaluation framework dependencies

# Or using pip
pip install .                  # core MCP server only
pip install ".[eval]"          # include evaluation framework dependencies

MCP Server Setup

To use MARRVEL-MCP with Claude Desktop, LM Studio, or other MCP-compatible clients, add the following to your client's MCP configuration:

{
  "mcpServers": {
    "marrvel-mcp": {
      "command": "/path/to/your/.venv/bin/python",
      "args": ["/path/to/MARRVEL_MCP/server.py"]
    }
  }
}

Replace the paths with the actual locations of your Python virtual environment and the cloned repository.

Usage

Ask your AI assistant natural language questions about genes, variants, diseases, orthologs, and literature. For example test cases, see mcp_llm_test/test_cases.yaml.

Features

MARRVEL-MCP provides 35+ MCP tools for genetics research:

• Gene queries - by symbol, Entrez ID, or genomic position
• Variant analysis - dbNSFP, ClinVar, gnomAD, DGV, Geno2MP
• Disease associations - OMIM, HPO, DECIPHER
• Ortholog information - DIOPT across model organisms
• Expression data - GTEx, Pharos drug targets, STRING interactions
• Literature search - PubMed, PMC full text/tables/figures
• Coordinate conversion - hg19/hg38 liftover

See docs/TOOL_RELATIONSHIPS.md for a visual diagram of tool chains and workflows.

Documentation

Document	Description
mcp_llm_test/README.md	Evaluation framework for benchmarking LLMs with MARRVEL-MCP
docs/TOOL_RELATIONSHIPS.md	Tool relationship graph and common analysis chains
marrvel_mcp/README.md	Package API reference for the marrvel_mcp module
tests/README.md	Test suite overview and instructions

Development

# Install with dev dependencies
uv sync --group dev --extra eval

# Run tests
pytest tests/

# Format code
black .

Citation

Wang J, et al. (2017) MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. Am J Hum Genet 100(6):843-853.

Support

• Website: https://marrvel.org
• API Docs: https://marrvel.org/doc