nickzren/mygene-mcp
3.1
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The MyGene MCP Server is a Model Context Protocol server that provides AI assistants with access to the MyGene.info API, offering a wide range of gene-related data and tools.
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
Development
uv run pytest tests/ -v