# pubcrawl

Search papers, drug labels, and clinical trials from an AI assistant through MCP. Useful when answers need traceable primary sources.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 15
- Author: nickjlamb
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/nickjlamb/pubcrawl
- Updated: 2026-10-16
- HTML: https://affpapa.org/en/nevibecode/mcp/pubcrawl

## What it does

pubcrawl connects an AI assistant to PubMed, Europe PMC, FDA and UK drug labelling, and ClinicalTrials.gov. It can search papers, retrieve structured abstracts and open-access full text, find related work, and format citations. Drug tools cover name resolution, US Prescribing Information, UK SmPC data, and side-by-side label comparison.

The server exposes 14 tools backed by source APIs, with identifiers such as PMIDs, NCT IDs, and DOIs for verification. It runs through `npx`, so there is no separate package installation step. An NCBI API key is optional; adding one raises PubMed request limits, which matters for repeated searches.

## Requirements
- Needs: Node.js (commands run via npx)
- Environment variables: `NCBI_API_KEY` — keys and tokens: ask the human for the values, never commit them or put them in shared files.

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add pubcrawl -e NCBI_API_KEY=<NCBI_API_KEY> -- npx -y @pharmatools/pubcrawl
```
Replace <…> with your own values

### Codex

**Platform CLI**
```bash
codex mcp add pubcrawl --env NCBI_API_KEY=<NCBI_API_KEY> -- npx -y @pharmatools/pubcrawl
```
Replace <…> with your own values

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "pubcrawl": {
            "command": "npx",
            "args": [
                "-y",
                "@pharmatools/pubcrawl"
            ],
            "env": {
                "NCBI_API_KEY": "<NCBI_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "pubcrawl": {
            "type": "stdio",
            "command": "npx",
            "args": [
                "-y",
                "@pharmatools/pubcrawl"
            ],
            "env": {
                "NCBI_API_KEY": "<NCBI_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add -e NCBI_API_KEY=<NCBI_API_KEY> pubcrawl npx -y @pharmatools/pubcrawl
```
Replace <…> with your own values

## When to use it
- search PubMed with date and article-type filters
- find preprints and open-access papers in Europe PMC
- compare US and UK drug labelling
- retrieve related studies and format citations

## Example prompts
- Search PubMed for studies on semaglutide and cardiovascular outcomes, then return the PMID and DOI.
- Compare the US and UK labels for atorvastatin and find its Phase 3 clinical trials.
- Get the structured abstract for an article by PMID and format the citation in Vancouver style.

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