Overview
Biomart MCP is a server that interfaces with Biomart, utilizing the Model Context Protocol (MCP) to standardize how applications provide context to large language models (LLMs).
To use Biomart MCP, clone the repository from GitHub, install the necessary dependencies, and run the server using the provided commands. You can also integrate it with other models via Cursor's agent mode.
- Mart and Dataset Discovery: List available marts and datasets in the Biomart database. - Attribute and Filter Exploration: View available attributes and filters for specific datasets. - Data Retrieval: Query Biomart for biological data using specific attributes and filters. - ID Translation: Convert between different biological identifiers.
- Researchers can retrieve biological data for analysis.
- Developers can integrate Biomart data into applications.
- Educators can use it to demonstrate biological data retrieval techniques.
Add to your AI client
Use these steps to connect Biomart MCP in Cursor, Claude, VS Code, and other MCP-compatible apps. The same JSON appears in the Use with menu above for one-click copy.
Cursor
Add this to your .cursor/mcp.json file in your project root, then restart Cursor.
.cursor/mcp.json
{
"mcpServers": {
"biomart-mcp-jzinno": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-biomart-mcp-jzinno"
]
}
}
}Claude Desktop
Add this server entry to the mcpServers object in your Claude Desktop config, then restart the app.
~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows)
{
"mcpServers": {
"biomart-mcp-jzinno": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-biomart-mcp-jzinno"
]
}
}
}Claude Code
Add this to your project's .mcp.json file. Claude Code will detect it automatically.
.mcp.json (project root)
{
"mcpServers": {
"biomart-mcp-jzinno": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-biomart-mcp-jzinno"
]
}
}
}VS Code (Copilot)
Add this to your .vscode/mcp.json file. Requires the GitHub Copilot extension with MCP support enabled.
.vscode/mcp.json
{
"servers": {
"biomart-mcp-jzinno": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-biomart-mcp-jzinno"
]
}
}
}Windsurf
Add this to your Windsurf MCP config file, then restart Windsurf.
~/.codeium/windsurf/mcp_config.json
{
"mcpServers": {
"biomart-mcp-jzinno": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-biomart-mcp-jzinno"
]
}
}
}Cline
Open Cline settings, navigate to MCP Servers, and add this server configuration.
Cline MCP Settings (via UI)
{
"mcpServers": {
"biomart-mcp-jzinno": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-biomart-mcp-jzinno"
]
}
}
}FAQ
What is the Model Context Protocol (MCP)?
MCP is an open protocol that standardizes how applications provide context to LLMs.
Can I contribute to Biomart MCP?
Yes! Contributions are welcome through pull requests on GitHub.
What programming language is Biomart MCP written in?
Biomart MCP is written in Python.