Pubcrawl

An [MCP server](https://modelcontextprotocol.io) that gives AI assistants access to PubMed, Europe PMC, FDA & UK drug labelling, and ClinicalTrials.gov.

_A peer-reviewed pub crawl through the literature — the label — and the trial._

Quick start · Tools · Examples · Architecture · Self-hosting · Roadmap · Contributing

✨ What is PubCrawl?

PubCrawl connects your AI assistant (Claude Desktop, Cursor, or any MCP-compatible client) directly to the primary sources clinicians and researchers actually use — so you can ask a question in plain English and get an answer grounded in PubMed, Europe PMC, FDA/UK drug labelling, and ClinicalTrials.gov, with real PMIDs, NCT IDs, and DOIs you can verify.

Every tool is a thin, deterministic wrapper over an official API. Nothing is invented; every result cites its source.

The thing no other MCP server does

Ask "compare US and UK labelling for semaglutide" and PubCrawl pulls both live labels and maps equivalent sections — US *Indications and Usage* ↔ UK *4.1 Therapeutic indications*, and so on — so the differences are visible instead of assumed:

A cardiovascular claim that is on-label in the US promotes an unlicensed indication in the UK. If you write, review, or check medical copy for both markets, that gap is the whole job — and compare_labels is the only MCP tool that surfaces it.

Everything else

• 🔬 14 tools across literature, drug labelling, and clinical trials
• 🧾 Verifiable by design — results link back to DailyMed, the eMC, PubMed, and ClinicalTrials.gov
• 📰 Preprints via Europe PMC — surface work ahead of formal publication
• 🆓 No API keys required (an optional free NCBI key raises PubMed rate limits)
• 🧪 Fully typed, tested, and CI-checked — literature retrieval gated by OpenGATE, and labelling & trials by the in-repo fidelity benchmark, on every release

Built by PharmaTools.AI.

🚀 Quick start (60 seconds)

1. Add PubCrawl to your client config — no install step needed, npx fetches it on first run.

For Claude Desktop, edit claude_desktop_config.json:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json

{

"mcpServers": { "pubcrawl": { "command": "npx", "args": ["-y", "@pharmatools/pubcrawl"] } } }

2. Restart your client. PubCrawl appears under + → Connectors.

3. Ask away:

_"Compare the US and UK labelling for atorvastatin, and find recent Phase 3 trials for it."_

That's it. → More examples · API key & other options

🧰 Tools

📚 Literature

💊 Drug labelling

🧫 Clinical trials

💬 Examples

Once connected, just ask naturally:

Literature

• "Search PubMed for recent clinical trials on semaglutide."
• "Search Europe PMC for preprints on GLP-1 receptor agonists, most cited first."
• "Get the abstract for PMID 38127654, then find related papers and cite them all in Vancouver style."
• "What are the trending papers on CRISPR gene therapy this month, high-impact journals only?"
• "Pull the full text of that PMC article and summarise the methods section."

Drug labelling

• "Get the FDA prescribing information for metformin — just the indications and warnings."
• "Pull the UK SmPC for atorvastatin."
• "Compare US and UK labelling for lisinopril and highlight the differences."
• "What's the generic name and drug class for Ozempic?"
• "What drugs are approved for type 2 diabetes in both the US and UK?"

Clinical trials

• "Find recruiting Phase 3 trials for pembrolizumab in breast cancer."
• "Get the eligibility criteria and primary outcomes for NCT03086486."

Cross-source (where PubCrawl shines)

• "For semaglutide: summarise the US label's cardiovascular indication, then find the pivotal trial and its NEJM publication."

🏗 Architecture

Three layers — tools register the MCP interface, lib clients talk to each external API, and shared cache + parsers keep it fast and consistent.

Each tool file exports a register*Tool(server) function with a zod schema and an async handler. All network calls are rate-limited, cached, and time-bounded. See CLAUDE.md for a full architecture walkthrough and CONTRIBUTING.md to add a tool.

🔧 Configuration

Install options

# Zero-install (recommended): npx fetches it on demand — see Quick start above.

Or install globally:

npm install -g @pharmatools/pubcrawl

Config for a global install:

{ "mcpServers": { "pubcrawl": { "command": "pubcrawl" } } }

NCBI API key (optional)

Without a key, PubMed requests are limited to 3/second. A free key raises this to 10/second.

1. Create a free NCBI account at https://www.ncbi.nlm.nih.gov/account/
2. Account Settings → API Key Management → create a key
3. Add it to your config:

{

"mcpServers": { "pubcrawl": { "command": "npx", "args": ["-y", "@pharmatools/pubcrawl"], "env": { "NCBI_API_KEY": "your_key_here" } } } }

HTTP transport

PubCrawl also ships a stateless Streamable HTTP transport for hosted and browser-based clients:

npm run start:http   # serves POST /mcp and GET /health on PORT (default 3000)

🏢 Run in your own environment

For teams who need PubCrawl inside their own cloud project rather than on a laptop, it runs as a container serving MCP over Streamable HTTP. Each request is handled by a fresh server instance with no sessions, so it scales horizontally behind any load balancer.

docker build -t pubcrawl .

docker run --rm -p 8080:8080 pubcrawl curl http://localhost:8080/health # {"status":"ok","server":"pubcrawl","version":"…"}

Point any MCP client, or an agent registry such as Google Cloud Agent Registry, Microsoft Foundry or Amazon Bedrock AgentCore, at https:// /mcp. Authentication is left to the platform in front of the container (Cloud Run IAM, API Gateway, an identity-aware proxy), so PubCrawl itself holds no credentials for your users.

The image runs as a non-root user, has