bioruby-mcp-server

A Model Context Protocol (MCP) server that provides access to BioRuby KEGG functionality. This server allows AI assistants to query KEGG databases for biological pathways, compounds, enzymes, and other molecular information through the standardized MCP protocol.

Built using the official MCP Ruby SDK.

Installation

Add this line to your application's Gemfile:

gem 'bioruby-mcp-server'

And then execute:

$ bundle install

Or install it yourself as:

$ gem install bioruby-mcp-server

Usage

Starting the Server

To start the MCP server:

$ bioruby-mcp-server

The server will start and listen for MCP protocol messages on stdin/stdout.

Available Tools

The server provides the following tools for interacting with KEGG databases:

1. kegg_pathway_info

Get detailed information about a KEGG pathway.

Parameters:

• pathway_id (string): KEGG pathway ID (e.g., 'map00010', 'hsa00010')

Example:

{
  "name": "kegg_pathway_info",
  "arguments": {
    "pathway_id": "map00010"
  }
}

2. kegg_compound_info

Get detailed information about a KEGG compound.

Parameters:

• compound_id (string): KEGG compound ID (e.g., 'C00002', 'cpd:C00002')

Example:

{
  "name": "kegg_compound_info",
  "arguments": {
    "compound_id": "C00002"
  }
}

3. kegg_enzyme_info

Get detailed information about a KEGG enzyme.

Parameters:

• enzyme_id (string): KEGG enzyme ID (e.g., 'ec:1.1.1.1')

Example:

{
  "name": "kegg_enzyme_info",
  "arguments": {
    "enzyme_id": "ec:1.1.1.1"
  }
}

4. kegg_search_compounds

Search for KEGG compounds by name or formula.

Parameters:

• query (string): Search query (compound name, formula, etc.)
• database (string, optional): Database to search (default: 'compound')

Example:

{
  "name": "kegg_search_compounds",
  "arguments": {
    "query": "glucose",
    "database": "compound"
  }
}

5. kegg_find_pathways_by_compound

Find pathways containing a specific compound.

Parameters:

• compound_id (string): KEGG compound ID (e.g., 'C00002')

Example:

{
  "name": "kegg_find_pathways_by_compound",
  "arguments": {
    "compound_id": "C00002"
  }
}

6. kegg_list_organisms

List available organisms in KEGG.

Parameters:

• filter (string, optional): Optional filter for organism names

Example:

{
  "name": "kegg_list_organisms",
  "arguments": {
    "filter": "human"
  }
}

Integration with AI Assistants

This MCP server can be used with any AI assistant that supports the Model Context Protocol. Configure your AI assistant to connect to this server to enable KEGG database queries.

Claude Desktop Integration

To connect this server to Claude Desktop, you'll need to configure it in Claude's MCP settings:

1. Install the Server

First, install the bioruby-mcp-server gem:

gem install bioruby-mcp-server

2. Configure Claude Desktop

Add the server configuration to Claude Desktop's configuration file:

On macOS: Edit or create ~/Library/Application Support/Claude/claude_desktop_config.json

On Windows: Edit or create %APPDATA%\Claude\claude_desktop_config.json

On Linux: Edit or create ~/.config/Claude/claude_desktop_config.json

Add the following configuration:

{
  "mcpServers": {
    "bioruby-kegg": {
      "command": "bioruby-mcp-server",
      "args": []
    }
  }
}

If you are Windows WSL user:

{
  "mcpServers": {
    "bioruby-kegg": {
			"command": "wsl.exe",
			"args": [
				"bioruby-mcp-server"
			]
    }
  }
}

3. Restart Claude Desktop

After saving the configuration file, restart Claude Desktop to load the new MCP server.

4. Verify Connection

Once connected, you can test the integration by asking Claude to query KEGG databases. For example:

• "Ge

... View full README on GitHub