{"id":"5d25cd48-3da3-44aa-9de2-fdd94202f3b3","slug":"nickzren-monarch-mcp","kind":"mcp","name":"monarch-mcp","summary":"MCP server for Monarch Initiative Data","owner":"nickzren","repoUrl":"https://github.com/nickzren/monarch-mcp","license":"MIT","licenseTier":"permissive","trust":"community","stars":0,"match":null,"fewStars":true,"format":"mcp","createdAt":"2025-06-10T15:16:43.000Z","addedAt":"2026-10-21T04:00:59.140Z","logoUrl":"https://avatars.githubusercontent.com/u/6598524?u=6cd7a812bb05f8ac754a7f662014bdf3942c14a9&v=4","linkOnly":false,"collection":null,"skillPath":null,"categories":["cloud-infra","memory-knowledge","data-analytics"],"tags":["bioinformatics","biomedical","fastmcp","genomics","hpo","knowledge-graph","monarch-initiative","mondo"],"runtime":"binary","local":true,"cloudCapable":false,"cloudCapability":"unknown","cloudReadyOnPlatform":false,"needsApiKey":false,"reviewed":false,"syncedAt":"2026-10-23T20:15:06.100Z","sample":false,"url":"https://conduits.dev/tools/nickzren-monarch-mcp","language":"Python","transports":["stdio"],"install":{},"requirements":{"env":[],"upstreamMayCharge":false},"tools":null,"readme":"# Monarch MCP Server\n\n[![CI](https://github.com/nickzren/monarch-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/nickzren/monarch-mcp/actions/workflows/ci.yml)\n[![Python 3.12+](https://img.shields.io/badge/python-3.12%2B-blue.svg)](https://www.python.org/downloads/)\n[![FastMCP 2.14.5+ <3](https://img.shields.io/badge/FastMCP-2.14.5%2B%20%3C3-0b7285.svg)](https://pypi.org/project/fastmcp/)\n[![License: MIT](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)\n\nA Model Context Protocol (MCP) server that exposes the Monarch Initiative API as a set of tools.\n\n## Features\n\n### Core Capabilities\n\n- **Entity Search**: Query genes, diseases, phenotypes across 33 integrated biomedical resources\n- **Phenotype Matching**: Find similar diseases using semantic similarity algorithms\n- **Cross-Species Analysis**: Explore gene-phenotype-disease relationships across human and model organisms\n- **Association Discovery**: Navigate connections between genes, diseases, phenotypes, chemicals, and variants\n- **Clinical Diagnostics**: Support rare disease diagnosis through phenotype profile matching\n- **Ontology Mapping**: Translate between different biomedical nomenclatures (OMIM, MONDO, HP, etc.)\n- **Chemical/Drug Data**: Access drug-disease relationships and treatment information\n\n### Data Sources\n\nThe Monarch Knowledge Graph integrates 33 biomedical resources:\n\n- **Clinical/Genetics**: OMIM, Orphanet, ClinVar, HGNC, HPO (Human Phenotype Ontology)\n- **Model Organisms**: Alliance of Genome Resources (MGI, ZFIN, WormBase, FlyBase, Xenbase, RGD), dictyBase, PomBase, SGD\n- **Ontologies**: MONDO (diseases), Gene Ontology, Uberon (anatomy), CHEBI (chemicals), PHENIO (cross-species phenotypes)\n- **Pathways & Interactions**: Reactome, STRING, BioGRID\n- **Expression**: Bgee (gene expression across species)\n- **Proteins**: UniProt\n- **Literature**: PubMed annotations\n- **Reference**: Ensembl, NCBI Gene\n\n## Prerequisites\n\n- Python 3.12+ with pip\n\n## Quick Start\n\n### 1. Install UV\nUV is a fast Python package and project manager.\n\n```bash\npip install uv\n```\n\n### 2. Install MCPM (MCP Manager)\nMCPM is a package manager for MCP servers that simplifies installation and configuration.\n\n```bash\npip install mcpm\n```\n\n### 3. Setup the MCP Server\n\nChoose one install mode:\n\nRuntime only:\n```bash\ncd monarch-mcp\nuv sync\n```\n\nRuntime + development + examples:\n```bash\ncd monarch-mcp\nuv sync --extra dev --extra examples\n```\n\nBy default, the server uses Monarch API `https://api.monarchinitiative.org/v3/api/`.\nSet `MONARCH_API_URL` only if you need a different endpoint.\n\n### 4. Add the Server to Claude Desktop\n```bash\n# Make sure you're in the project directory\ncd monarch-mcp\n\n# Set Claude as the target client\nmcpm target set @claude-desktop\n\n# Add the Monarch MCP server\nmcpm import stdio monarch \\\n  --command \"$(uv run which python)\" \\\n  --args \"-m monarch_mcp.server\"\n```\nThen restart Claude Desktop.\n\n## Usage\n\n#### Running the Server\n\n```bash\nuv run python -m monarch_mcp.server\n```\n\nYou can choose a specific transport when starting the FastMCP server:\n\n```bash\nuv run python -m monarch_mcp.server --transport stdio        # default (Claude Desktop)\nuv run python -m monarch_mcp.server --transport sse --host 0.0.0.0 --port 8000\nuv run python -m monarch_mcp.server --transport http --host 0.0.0.0 --port 8000\n```\n\nWhen running with `--transport sse` or `--transport http`, the server exposes a discovery document at `/.well-known/mcp.json` and a health check at `/`.\n\n#### AI Agent Example\n\n```bash\n# Create .env file with your OpenAI API key\ncat <<EOF > .env\nOPENAI_API_KEY=your_key_here\nOPENAI_MODEL=gpt-5-mini\nEOF\n\n# Run the example agent\nuv run --extra examples python examples/react_agent.py\n```\n\n#### Development\n\n```bash\n# Run tests\nuv run --extra dev pytest tests/ -v\n```\n"}