PubCrawl

An MCP server that gives LLM clients access to PubMed, FDA drug labelling, UK medicines data, and ClinicalTrials.gov. A peer-reviewed pub crawl through the literature — the label — and the trial.

Built by PharmaTools.AI.

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.
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
get_uspi	Pull US Prescribing Information sections from DailyMed — indications, dosing, warnings, contraindications, and more. Parsed from FDA structured product labels.
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.

Setup

Prerequisites

• Node.js 20+
• An MCP-compatible client (Claude Desktop, Cursor, etc.)

Install via npm

npm install -g @pharmatools/pubcrawl

Configure Claude Desktop

Add to your claude_desktop_config.json:

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

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

Restart Claude Desktop. PubCrawl will appear under + → Connectors.

Install from source

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

Then point the config at the built file:

{
  "mcpServers": {
    "pubcrawl": {
      "command": "node",
      "args": ["/path/to/pubcrawl/dist/index.js"]
    }
  }
}

NCBI API key (optional)

Without an API key, requests are rate-limited to 3/second. With one, you get 10/second.

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

{
  "mcpServers": {
    "pubcrawl": {
      "command": "pubcrawl",
      "env": {
        "NCBI_API_KEY": "your_key_here"
      }
    }
  }
}

Example prompts

Once connected, just ask naturally:

• "Search PubMed for recent clinical trials on semaglutide"
• "Get the abstract for PMID 38127654"
• "Find papers related to this one and format citations in APA"
• "What are the trending papers on CRISPR gene therapy this month?"
• "Get the full text of that paper from PMC"
• "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"
• "What drugs are approved for type 2 diabetes?"
• "Find recruiting Phase 3 trials for pembrolizumab in breast cancer"
• "Get details on clinical trial NCT03086486"

Development

npm run dev    # TypeScript watch mode
npm run build  # Compile to dist/
npm start      # Run the server

License

MIT