Pubcrawl README

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:

	US Prescribing Information	UK SmPC
Indications	glycaemic control · reduce risk of MACE in T2D with established CVD · reduce risk of sustained eGFR decline, ESKD and CV death in T2D with CKD	glycaemic control only — CV and renal outcomes appear as cross-references to §4.4/4.5/5.1, not as indications
Contraindications	personal or family history of MTC or MEN 2 · hypersensitivity	hypersensitivity only

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 — retrieval fidelity gated by OpenGATE 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

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

Tool	What it does
`search_pubmed`	Search PubMed with filters for date range, article type, and sort order. Returns PMIDs, titles, authors, journals, and DOIs.
`search_europepmc`	Search Europe PMC — a broader corpus than PubMed that also indexes preprints (bioRxiv, medRxiv) and patents. Each result includes an abstract snippet, citation count, open-access status, and a preprint flag. Filter to preprints or open-access only.
`get_abstract`	Get the full structured abstract for an article — broken into labeled sections (background, methods, results, conclusions) with keywords and MeSH terms.
`get_full_text`	Retrieve the full text of open-access articles from PubMed Central, with parsed sections, figure/table captions, and reference counts.
`find_related`	Find similar articles using PubMed's neighbor algorithm, ranked by relevance score.
`format_citation`	Generate a formatted citation in APA, Vancouver, Harvard, or BibTeX style.
`trending_papers`	Find recent papers on a topic, with optional filtering to high-impact journals (Nature, Science, Cell, NEJM, Lancet, JAMA, etc.).

💊 Drug labelling

Tool	What it does
`resolve_drug_name`	Convert a brand drug name to its generic (or a generic to its US brand names), with drug class and common indications. Deterministic, via RxNorm/openFDA — no AI.
`get_uspi`	Pull US Prescribing Information sections via openFDA (cited to DailyMed) — indications, dosing, warnings, contraindications, and more.
`get_smpc`	Retrieve UK Summary of Product Characteristics from the eMC — the UK equivalent of US prescribing information, with numbered SmPC sections.
`compare_labels`	Side-by-side comparison of US (USPI) and UK (SmPC) labelling for the same drug. Spot regulatory differences in indications, warnings, and dosing.
`search_by_indication`	Find drugs approved for a medical condition. Searches FDA labelling via openFDA, then cross-references UK availability on the eMC.

🧫 Clinical trials

Tool	What it does
`search_trials`	Search ClinicalTrials.gov for clinical trials. Filter by condition, intervention, recruitment status, and phase. Returns NCT IDs, sponsors, enrollment, and links.
`get_trial`	Get full details for a clinical trial by NCT ID — eligibility criteria, study design, arms, primary/secondary outcomes, locations, and associated PubMed IDs.

💬 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

bash

# 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.

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

config.json

{
  "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:

Terminal

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

bash

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, and formatting 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.

📦 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:

bibtex

@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

_{Data from NCBI E-utilities, Europe PMC, openFDA, DailyMed, the UK eMC, and ClinicalTrials.gov. PubCrawl is not affiliated with these providers.}