WormBase MCP Server

MCP server for querying WormBase - the C. elegans and nematode genomics database.

Installation

Claude Desktop

Add to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "wormbase": {
      "command": "npx",
      "args": ["-y", "@nuin/wormbase-mcp"]
    }
  }
}

Claude Code (CLI)

Add to ~/.claude/settings.json:

{
  "mcpServers": {
    "wormbase": {
      "command": "npx",
      "args": ["-y", "@nuin/wormbase-mcp"]
    }
  }
}

Cursor

Add to Cursor settings (Settings > MCP Servers):

{
  "wormbase": {
    "command": "npx",
    "args": ["-y", "@nuin/wormbase-mcp"]
  }
}

Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "wormbase": {
      "command": "npx",
      "args": ["-y", "@nuin/wormbase-mcp"]
    }
  }
}

From source

git clone https://github.com/WormBase/wormbase-mcp.git
cd wormbase-mcp
npm install && npm run build

Then use the local path in your config:

{
  "mcpServers": {
    "wormbase": {
      "command": "node",
      "args": ["/path/to/wormbase-mcp/dist/index.js"]
    }
  }
}

Usage

Just ask questions naturally:

• "What does daf-2 do?"
• "Search for genes involved in longevity"
• "Get phenotypes for unc-13"
• "Find interactions for lin-14"
• "What are the homologs of aap-1?"
• "Give me the sequence of protein CE29083"

Tools

Tool	Description
search	Search genes, proteins, phenotypes, strains
get_gene	Gene details (accepts names like daf-2 or IDs like WBGene00000898)
get_protein	Protein sequences and domains
get_phenotype	Phenotype info and associated genes
get_disease	Human disease models
get_strain	Laboratory strains
get_variation	Alleles and mutations
get_interactions	Genetic and physical interactions
get_expression	Expression patterns
get_ontology	GO annotations
get_paper	Publication details

Data Sources

• Search & name resolution: WormMine
• Detailed data: WormBase REST API

License

MIT