NIAID Data MCP Server

An MCP (Model Context Protocol) server for the NIAID Data Ecosystem API, enabling LLMs to search biomedical research resources — datasets, clinical studies, publications, repositories, and more — funded or supported by NIAID.

Tools

niaid_data_query

Search the NIAID Data Ecosystem using Elasticsearch query string syntax.

Parameters:

Example queries:

• q="COVID-19 AND @type:Dataset" — find COVID-19 datasets

• q="*", aggs=["@type"] — summarize resource types across the whole catalog

• q="malaria", sort="-date", size=20 — most recent malaria resources

Related MCP server: DataCite MCP Server

Setup

Requires Python 3.11+ and uv.

uv sync

Running as a stdio MCP server (for Claude Desktop / MCP clients)

uv run python main.py

Claude Desktop config (claude_desktop_config.json):

{
  "mcpServers": {
    "niaid-data": {
      "command": "uv",
      "args": ["run", "python", "main.py"],
      "cwd": "/path/to/niaid-data-mcp-server"
    }
  }
}

Running as an HTTP server

PORT=8000 uv run python main.py

A /health endpoint is available at http://localhost:8000/health.