# Pubcrawl

> A peer-reviewed pub crawl through the literature — MCP server for PubMed & biomedical literature search

- **Type:** MCP server
- **Install:** `agentstack add mcp-nickjlamb-pubcrawl`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [nickjlamb](https://agentstack.voostack.com/s/nickjlamb)
- **Installs:** 0
- **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [nickjlamb](https://github.com/nickjlamb)
- **Source:** https://github.com/nickjlamb/pubcrawl
- **Website:** https://www.pharmatools.ai/pubcrawl

## Install

```sh
agentstack add mcp-nickjlamb-pubcrawl
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# PubCrawl

An [MCP server](https://modelcontextprotocol.io) 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](https://pharmatools.ai).

[](https://github.com/nickjlamb/pubcrawl/actions/workflows/build.yml)
[](https://www.npmjs.com/package/@pharmatools/pubcrawl)
[](LICENSE)
[](https://registry.modelcontextprotocol.io/?q=pubcrawl)

## 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 |
|------|-------------|
| `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. |

## Setup

### Prerequisites

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

### Install via npm

```bash
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`

```json
{
  "mcpServers": {
    "pubcrawl": {
      "command": "pubcrawl"
    }
  }
}
```

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

### Install from source

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

Then point the config at the built file:

```json
{
  "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:

```json
{
  "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

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

## License

MIT

## Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [nickjlamb](https://github.com/nickjlamb)
- **Source:** [nickjlamb/pubcrawl](https://github.com/nickjlamb/pubcrawl)
- **License:** MIT
- **Homepage:** https://www.pharmatools.ai/pubcrawl

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/mcp-nickjlamb-pubcrawl
- Seller: https://agentstack.voostack.com/s/nickjlamb
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.