Niaid Data Server

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Enables searching the NIAID Data Ecosystem for biomedical research resources including datasets, clinical studies, and publications using Elasticsearch queries.

by mark-aronson

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About

Enables searching the NIAID Data Ecosystem for biomedical research resources including datasets, clinical studies, and publications using Elasticsearch queries.

README

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.

from github.com/mark-aronson/niaid-data-mcp-server

Install Niaid Data Server in Claude Desktop, Claude Code & Cursor

Recommended · one command, every IDE

unyly install niaid-data-mcp-server

Installs into Claude Desktop, Claude Code, Cursor & VS Code — handles npx, uvx and build-from-source repos for you.

First time? Get the CLI: curl -fsSL https://unyly.org/install | sh

Or configure manually

Run in your terminal:

claude mcp add niaid-data-mcp-server -- uvx --from git+https://github.com/mark-aronson/niaid-data-mcp-server niaid-data-mcp-server

FAQ

Is Niaid Data Server MCP free?

Yes, Niaid Data Server MCP is free — one-click install via Unyly at no cost.

Does Niaid Data Server need an API key?

No, Niaid Data Server runs without API keys or environment variables.

Is Niaid Data Server hosted or self-hosted?

A hosted option is available: Unyly runs the server in the cloud, no local setup required.

How do I install Niaid Data Server in Claude Desktop, Claude Code or Cursor?

Open Niaid Data Server on unyly.org, pick your client tab (Claude Desktop, Claude Code, Cursor) and press Install — the config is generated automatically, no JSON editing.

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