WormBase

Queries WormBase data for C. elegans and nematode genomics, enabling gene, phenotype, interaction, and sequence lookups through an MCP client.

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6 months ago

First Indexed

3 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

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

You can query WormBase data and related nematode genomics information by running a WormBase MCP Server. It exposes a focused set of endpoints you can access from your MCP client to search genes, proteins, phenotypes, strains, interactions, and more, all backed by WormBase data.

How to use

Ask natural questions to your MCP client to retrieve WormBase data. You can search for genes, proteins, phenotypes, and strains, fetch gene details, obtain protein sequences and domains, explore phenotypes and associated genes, look up interactions, get expression patterns, and retrieve GO annotations and publication details. Use descriptive queries like: ”What does daf-2 do?”, ”Search for genes involved in longevity”, ”Get phenotypes for unc-13”, ”Find interactions for lin-14”, or ”What are the homologs of aap-1?”.

How to install

Prerequisites: you need Node.js and npm installed on your system. Ensure you have a working internet connection to fetch dependencies.

Option 1: Run the MCP server via the standard MCP client integration (using npx) in the following environments.

Claude Desktop configuration

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

Claude Code (CLI) configuration

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

Cursor configuration

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

Windsurf configuration

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

Option 2: Build and run from source

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

After building, use the local runtime path in your config

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

What you can do with WormBase MCP Server

You can perform a wide range of queries to WormBase data through the MCP server, including gene details, protein sequences and domains, phenotypes, diseases models, strains, variations, interactions, expression patterns, GO annotations, and related publications.

Data sources

Data is drawn from WormMine for search and name resolution, and WormBase REST API for detailed data.

License

MIT license.

Available tools

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