MyGene MCP Server

A Model Context Protocol (MCP) server that exposes the MyGene.info API as a set of tools for AI assistants.

Features

Core Capabilities

• Gene Search: Query genes by symbol, name, Entrez ID, Ensembl ID, or other identifiers
• Gene Annotations: Retrieve comprehensive gene information from multiple sources
• Expression Queries: Search genes by tissue expression or retrieve expression profiles
• Pathway Queries: Find genes in biological pathways or get pathway memberships
• GO Annotations: Search by GO terms or retrieve GO annotations with evidence codes
• Disease Associations: Find disease-associated genes or get gene-disease links
• Drug/Chemical Interactions: Search genes by drug/chemical or get interaction data
• Ortholog/Homology: Find orthologs across species or search homologous genes
• Variant Information: Retrieve genetic variants and clinical significance
• Batch Operations: Process up to 1000 genes in a single request
• Genomic Interval Search: Find genes by chromosomal coordinates
• Advanced Queries: Build complex queries with boolean logic and filters
• Data Export: Export gene lists in TSV, CSV, JSON, or XML formats

Data Sources

• NCBI: Entrez Gene, RefSeq, HomoloGene
• Ensembl: Gene annotations, homology data
• UniProt: Protein annotations, GO terms
• Human Protein Atlas (HPA): Tissue expression, subcellular localization
• GTEx: Gene expression in human tissues
• BioGPS: Gene expression profiles
• ExAC: Exome aggregation data
• KEGG: Pathways and disease associations
• Reactome: Biological pathways
• WikiPathways: Community pathways
• BioCarta: Pathway diagrams
• NetPath: Signal transduction pathways
• PID: Pathway Interaction Database
• Gene Ontology: Functional annotations
• DisGeNET: Disease-gene associations
• ClinVar: Clinical variants
• OMIM: Genetic disorders
• PharmGKB: Pharmacogenomics
• DrugBank: Drug targets
• ChEMBL: Bioactive compounds
• ChEBI: Chemical entities
• InterPro: Protein families and domains
• Pfam: Protein families
• SMART: Protein domains
• PANTHER: Gene function classification

Prerequisites

• Python 3.12+ with pip

Quick Start

1. Install UV

UV is a fast Python package and project manager.

pip install uv

2. Install MCPM (MCP Manager)

MCPM is a package manager for MCP servers that simplifies installation and configuration.

pip install mcpm

3. Setup the MCP Server

cd mygene-mcp
uv sync

4. Add the Server to Claude Desktop

# Make sure you're in the project directory
cd mygene-mcp

# Set Claude as the target client
mcpm target set @claude-desktop

# Add the MyGene MCP server
mcpm import stdio mygene \
  --command "$(uv run which python)" \
  --args "-m mygene_mcp.server"

Then restart Claude Desktop.

Usage

Running the Server

uv run python -m mygene_mcp.server

You can choose a specific transport when starting the FastMCP server:

uv run python -m mygene_mcp.server --transport stdio        # default (Claude Desktop)
uv run python -m mygene_mcp.server --transport sse --host 0.0.0.0 --port 8000
uv run python -m mygene_mcp.server --transport http --host 0.0.0.0 --port 8000

When running with --transport sse or --transport http, the server exposes a discovery document at /.well-known/mcp.json and a health check at /.

Development

uv sync --extra dev
uv run pytest tests/ -v