WormBase MCP Server

# WormBase MCP Server MCP server for querying [WormBase](https://wormbase.org) - 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): ```json { "mcpServers": { "wormbase": { "command": "npx", "args": ["-y", "@nuin/wormbase-mcp"] } } } ``` ### Claude Code (CLI) Add to `~/.claude/settings.json`: ```json { "mcpServers": { "wormbase": { "command": "npx", "args": ["-y", "@nuin/wormbase-mcp"] } } } ``` ### Cursor Add to Cursor settings (Settings > MCP Servers): ```json { "wormbase": { "command": "npx", "args": ["-y", "@nuin/wormbase-mcp"] } } ``` ### Windsurf Add to `~/.codeium/windsurf/mcp_config.json`: ```json { "mcpServers": { "wormbase": { "command": "npx", "args": ["-y", "@nuin/wormbase-mcp"] } } } ``` ### From source ```bash 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: ```json { "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](https://wormmine.alliancegenome.org/wormmine) - **Detailed data**: [WormBase REST API](http://rest.wormbase.org) ## License MIT