medrxiv-mcp

MCP server that turns a medRxiv DOI into clean markdown full text — plus free, relevance-ranked preprint search.

• 📄 Full-text retrieval — give it a DOI, get the whole paper as clean markdown (sections, tables, figure captions)

• 🔍 Free search — relevance-ranked medRxiv search via Europe PMC, returns DOI + title + abstract + date

• 🩺 Source of truth — full text comes from the official medRxiv .meca Text-and-Data-Mining archive, not scraped HTML

• ⚡ Lazy local index — a DOI→file index is built on demand and cached in sqlite, so repeat fetches in a month are instant

• 🔓 Your data, your key — full text reads a Requester-Pays S3 bucket with your own AWS key; nothing is shipped or shared

bioRxiv has its own package: biorxiv-mcp.

What is this?

This is a Model Context Protocol (MCP) server that gives AI assistants the full text of medRxiv preprints. Search is free (via the Europe PMC REST API). Full text is resolved from the official s3://medrxiv-src-monthly archive: the server maps a DOI to its month, scans that month's .meca archives once to build a local DOI→file index, downloads the one matching archive, extracts its JATS XML, and converts it to GitHub-flavored markdown with pandoc.

Designed for AI assistants like Claude to read primary literature directly. Works with any MCP-compatible client (Claude Desktop, Claude Code, or custom integrations).

Related MCP server: medRxiv-MCP-Server

Installation

uvx --from git+https://github.com/yogsoth-ai/medrxiv-mcp medrxiv-mcp

No manual install needed — uvx fetches and runs it. The bundled pandoc binary ships with the package, so you do not need a system pandoc.

Quick Start

1. Add to your MCP client

Claude Code — .mcp.json in your project root Claude Desktop — claude_desktop_config.json (~/Library/Application Support/Claude/ on macOS, %APPDATA%\Claude\ on Windows)

{
  "mcpServers": {
    "medrxiv": {
      "command": "uvx",
      "args": ["--from", "git+https://github.com/yogsoth-ai/medrxiv-mcp", "medrxiv-mcp"],
      "env": {
        "AWS_ACCESS_KEY_ID": "<your key id>",
        "AWS_SECRET_ACCESS_KEY": "<your secret>",
        "AWS_DEFAULT_REGION": "us-east-1"
      }
    }
  }
}

2. Supply your AWS key

search_preprints is free and needs no key. fetch_fulltext reads a Requester-Pays bucket and does — see below.

3. Restart your MCP client

The server starts automatically when the client needs it.

Requires your own AWS key (Requester-Pays)

medRxiv full text is only reliably reachable through the official s3://medrxiv-src-monthly Text-and-Data-Mining bucket, which is Requester-Pays: you supply an AWS key, and your account pays the (tiny) transfer cost. The package never ships a key — each user brings their own.

Costs are small:

Setup: in the AWS IAM console, create a user, attach the AmazonS3ReadOnlyAccess policy, create an access key, and put it in the env block above. Deactivate the key whenever you're done.

Optional env:

Available Tools

The intended workflow: search_preprints to find a paper and get its DOI cheaply, then fetch_fulltext on that DOI when you want to read it.

Example Queries

Ask Claude things like:

• "Search medRxiv for recent preprints on long-COVID cardiovascular outcomes and summarize the top 3 abstracts"

• "Fetch the full text of a medRxiv DOI and walk me through its statistical methods"

• "Find preprints on a vaccine-efficacy trial, then read the most relevant one in full"

For Developers

git clone https://github.com/yogsoth-ai/medrxiv-mcp.git
cd medrxiv-mcp
pip install -e .
python -m pytest -v          # offline suite — no AWS, no network
python -m medrxiv_mcp.server # run the server locally (needs AWS env for fetch)

The offline test suite covers the non-trivial logic (JATS→markdown conversion and the .meca DOI parser) against fixtures it builds itself — no AWS spend, no network. Live search and S3 fetch are smoke-tested manually.

Links

• 🐙 GitHub repository

• 🧬 biorxiv-mcp — the bioRxiv twin

• 🌐 Europe PMC REST API

• 📦 medRxiv TDM / Open Access

• 🔧 Model Context Protocol

📄 License

Apache-2.0