生物医学检索MCP服务

An MCP server 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 · 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 browser-based and hosted clients:

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

🗺 Roadmap

Highlights of what's planned — see ROADMAP.md for the full list.

• get_europepmc_fulltext — read preprints & OA articles surfaced by search_europepmc
• get_adverse_events — openFDA FAERS adverse-event lookups
• EMA / EPAR labelling to complement the US + UK compare_labels
• MeSH query helper for sharper PubMed searches
• MCP resources & prompts for common review workflows

Ideas welcome — open an issue.

🛠 Development

git clone https://github.com/nickjlamb/pubcrawl.git
cd pubcrawl
npm install

npm run dev      # TypeScript watch mode
npm run build    # compile to dist/
npm start        # run the stdio server
npm test         # Vitest unit suite
npm run lint     # ESLint

Unit tests live in tests/ and cover the parsing, caching, citation, formatting and label-pairing logic with fixture payloads (no network calls). CI runs lint → test → build on every push and pull request. New to the codebase? Start with CONTRIBUTING.md.

Measuring fidelity

npm run bench            # labelling + trials fidelity benchmark against the live sources
npm run bench -- --ci    # what the release gate runs: exit 1 if a verified case fails

Two gates run on every release and weekly. OpenGATE's retrieval scorer checks PubMed and Europe PMC records against hand-verified anchors. The in-repo fidelity benchmark does the same for drug labelling and trials: compare_labels is held to a gold set of US/UK anchors (a phrase must appear on one side and must not on the other, so real divergences are surfaced rather than smoothed over) plus a verbatim check that refetches the raw openFDA record and eMC page and confirms every returned sentence is a substring of the source. No LLM judge anywhere in either gate.

📦 Releases & changelog

Versions follow Semantic Versioning. See the CHANGELOG for a full history and Releases for notes and assets.

🤝 Contributing

Contributions are welcome and appreciated — bug reports, new data sources, new tools. Read the contributing guide to get started, then open an issue or a pull request.

📚 Citation

If PubCrawl supports work you publish, please cite it — see CITATION.cff, or:

@software{lamb_pubcrawl,
  author    = {Lamb, Nick},
  title     = {PubCrawl: verifiable biomedical literature, drug labelling and clinical trials for AI assistants},
  year      = {2026},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.22101559},
  url       = {https://doi.org/10.5281/zenodo.22101559}
}

📄 License

MIT © PharmaTools.AI