MCP Servers

niaid-data-mcp-server

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

README

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.

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