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