WormBase MCP Server

Name: WormBase MCP Server
Author: WormBase

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

Installation

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"] } } }

Add to ~/.claude/settings.json:

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

Add to Cursor settings (Settings > MCP Servers):

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

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

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

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"] } } }

Just ask questions naturally:

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