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