UCSC Genome Browser MCP Server

Instructions

Implementation Reference

• ucsc-genome-mcp.py:423-435 (handler)

  Handler function for get_track_data tool: maps input arguments to API parameters and calls the UCSC Genome API /getData/track endpoint.

  elif name == "get_track_data":
      params = {
          "genome": arguments["genome"],
          "track": arguments["track"],
          "chrom": arguments.get("chrom"),
          "start": arguments.get("start"),
          "end": arguments.get("end"),
          "hubUrl": arguments.get("hub_url"),
          "maxItemsOutput": arguments.get("max_items"),
          "jsonOutputArrays": 1 if arguments.get("json_output_arrays") else None
      }
      url = build_api_url("/getData/track", params)
      result = await make_api_request(url)

• ucsc-genome-mcp.py:267-308 (schema)

  Schema definition for the get_track_data tool, including input parameters like genome, track, optional chrom, start, end, hub_url, max_items, and json_output_arrays.

  Tool(
      name="get_track_data",
      description="Retrieve data from a specified track in a hub or UCSC database genome. Can be filtered by chromosome and coordinates.",
      inputSchema={
          "type": "object",
          "properties": {
              "genome": {
                  "type": "string",
                  "description": "Genome assembly name"
              },
              "track": {
                  "type": "string",
                  "description": "Track name"
              },
              "chrom": {
                  "type": "string",
                  "description": "Chromosome name (optional)"
              },
              "start": {
                  "type": "integer",
                  "description": "Start coordinate (0-based, optional, requires end)"
              },
              "end": {
                  "type": "integer",
                  "description": "End coordinate (1-based, optional, requires start)"
              },
              "hub_url": {
                  "type": "string",
                  "description": "URL of track/assembly hub (optional)"
              },
              "max_items": {
                  "type": "integer",
                  "description": "Maximum number of items to return (default: 1000000)"
              },
              "json_output_arrays": {
                  "type": "boolean",
                  "description": "Return data as JSON arrays instead of objects"
              }
          },
          "required": ["genome", "track"]
      }
  ),

• ucsc-genome-mcp.py:27-37 (helper)

  Helper function to construct the full UCSC API URL from endpoint and parameters, filtering None values and using semicolon separators.

  def build_api_url(endpoint: str, params: dict[str, Any]) -> str:
      """Build the complete API URL with parameters."""
      # Filter out None values
      filtered_params = {k: v for k, v in params.items() if v is not None}
      
      # Convert parameters to URL format (using semicolons as per UCSC API spec)
      if filtered_params:
          param_str = ";".join(f"{k}={v}" for k, v in filtered_params.items())
          return f"{BASE_URL}{endpoint}?{param_str}"
      return f"{BASE_URL}{endpoint}"

• ucsc-genome-mcp.py:39-45 (helper)

  Helper function to perform asynchronous HTTP GET request to UCSC API URL and parse JSON response.

  async def make_api_request(url: str) -> dict[str, Any]:
      """Make an HTTP request to the UCSC API and return JSON response."""
      async with httpx.AsyncClient(timeout=30.0) as client:
          response = await client.get(url)
          response.raise_for_status()
          return response.json()