WormBase MCP Server

WormBase MCP Server

Enables querying the WormBase database for C. elegans and nematode genomics data, including gene information, protein sequences, phenotypes, interactions, and expression patterns through natural language.

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README

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

License

MIT

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