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:

Parameter	Type	Default	Description
q	string	*	Elasticsearch query string. Supports field-specific queries, boolean operators, and wildcards.
size	int	10	Number of results to return (1–1000).
offset	int	0	Number of results to skip (for pagination).
sort	string	—	Sort field; prefix with - for descending (e.g., -date).
fields	string	—	Comma-separated fields to return (e.g., name,description,@type).
aggs	list[string]	—	Fields to aggregate/facet by (e.g., ["@type", "conditionsOfAccess"]).
facet_size	int	10	Max aggregation buckets per field (1–1000).
explain	bool	—	Include relevance score explanation.
response_format	string	markdown	markdown for readable output, json for structured data.

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

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.