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dbSNP MCP Plugin

Source

My attempt at an MCP server for dbSNP.

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Overview

The dbSNP MCP Plugin is a tool that allows developers to retrieve genetic variant information from NCBI's dbSNP database directly within their development environment.

To use the dbSNP MCP Plugin, install the required dependencies, set up the MCP server, and use the provided functions to retrieve SNP information by rs ID or search for SNPs using various terms.

  • Retrieve detailed information about SNPs using rs IDs. - Search for SNPs by gene names, phenotypes, and other terms. - Access clinical significance information for genetic variants.
  1. Researchers can quickly access SNP data for genetic studies.
  2. Developers can integrate SNP retrieval into bioinformatics applications.
  3. Clinicians can obtain clinical significance data for variants in patient reports.

Add to your AI client

Use these steps to connect dbSNP MCP Plugin 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": {
    "mcp-server-mattshu0410": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-mcp-server-mattshu0410"
      ]
    }
  }
}

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": {
    "mcp-server-mattshu0410": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-mcp-server-mattshu0410"
      ]
    }
  }
}

Claude Code

Add this to your project's .mcp.json file. Claude Code will detect it automatically.

.mcp.json (project root)

{
  "mcpServers": {
    "mcp-server-mattshu0410": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-mcp-server-mattshu0410"
      ]
    }
  }
}

VS Code (Copilot)

Add this to your .vscode/mcp.json file. Requires the GitHub Copilot extension with MCP support enabled.

.vscode/mcp.json

{
  "servers": {
    "mcp-server-mattshu0410": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-mcp-server-mattshu0410"
      ]
    }
  }
}

Windsurf

Add this to your Windsurf MCP config file, then restart Windsurf.

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "mcp-server-mattshu0410": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-mcp-server-mattshu0410"
      ]
    }
  }
}

Cline

Open Cline settings, navigate to MCP Servers, and add this server configuration.

Cline MCP Settings (via UI)

{
  "mcpServers": {
    "mcp-server-mattshu0410": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-mcp-server-mattshu0410"
      ]
    }
  }
}

FAQ

What are the prerequisites for using the dbSNP MCP Plugin?

You need Python 3.7+ and the MCP CLI tool installed.

How can I increase my request rate limit?

Obtain an NCBI API key and configure it in your setup to increase the limit from 3 to 10 requests per second.

What should I do if I encounter issues?

Check your internet connection, verify the rs ID format, ensure your API key is valid, and review error messages for specific issues.7:["$","div",null,{"className":"container mx-auto flex flex-col gap-4","children":["$L26","$L27",["$","$L28",null,{"currentProject":{"id":2228,"uuid":"28c62ace-097a-4529-bd0a-9b02e637ad80","name":"MCP-server","title":"dbSNP MCP Plugin","description":"My attempt at an MCP server for dbSNP.","avatar_url":"https://avatars.githubusercontent.com/u/62276229?v=4","created_at":"2025-03-09T04:25:26.122Z","updated_at":"2025-03-12T10:20:30.836Z","status":"created","author_name":"mattshu0410","author_avatar_url":"https://avatars.githubusercontent.com/u/62276229?v=4","tags":"dbsnp,genetic-variant,mcp-plugin","category":"research-and-data","is_featured":false,"sort":1,"url":"https://github.com/mattshu0410/MCP-server","target":"_self","content":"$29","summary":"$2a","img_url":null,"type":null,"metadata":"{\"star\":\"0\",\"license\":\"\",\"language\":\"Python\",\"is_official\":false,\"latest_commit_time\":\"2025-03-07 17:11:31\"}","user_uuid":null,"tools":null,"sse_url":null,"sse_provider":null,"sse_params":null,"is_official":false,"server_command":null,"server_params":null,"server_config":null,"allow_call":false,"is_innovation":false,"is_dxt":false,"dxt_manifest":null,"dxt_file_url":null,"is_audit":false},"randomProjects":[],"currentServerKey":"$undefined"}]]}]

Research and data