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MCP Server Setup (Optional but Recommended)

MCP = Model Context Protocol. MCP servers let Claude Code read your Zotero library, your Google Drive files, or live PubMed results directly. Each server is a separate install + one claude mcp add command.

You can use MedSci Skills without any MCP servers — they fall back to local files and public APIs. MCPs just make integration smoother (e.g., lit-sync skill is much faster with the Zotero MCP).

Zotero MCP (highest value for paper writing)

Why: lit-sync, verify-refs, and write-paper all benefit from direct Zotero access (read your library, add new items by DOI, sync references to manuscripts).

Install (Mac/Linux/Windows):

# Make sure Zotero desktop is running and you have an API key
# Get API key: https://www.zotero.org/settings/keys → Create new private key
# Save your library ID: visible in https://www.zotero.org/settings/keys

claude mcp add zotero --scope user \
  -e ZOTERO_LOCAL=true \
  -e ZOTERO_API_KEY=<your-api-key> \
  -e ZOTERO_LIBRARY_ID=<your-library-id> \
  -- npx zotero-mcp

Verify:

claude mcp list | grep zotero

Expected: zotero ✓ Connected

Google Drive / Workspace MCP

Why: Read/write Google Docs, Sheets, Drive files. Useful if your data lives in Google Sheets or your manuscripts are shared via Google Docs.

claude mcp add gdrive --scope user -- npx @modelcontextprotocol/server-gdrive

First run will prompt you to authenticate via browser (OAuth).

PubMed MCP (alternative to built-in search-lit)

Why: Slightly faster and richer than the E-utilities fallback in search-lit.

claude mcp add pubmed --scope user -- npx pubmed-mcp

No API key required for basic searches. For higher rate limits, add -e NCBI_API_KEY=<your-key> (get one at https://www.ncbi.nlm.nih.gov/account/settings/).

Filesystem MCP (built-in, usually pre-configured)

Claude Code ships with filesystem access by default. If you've disabled it, re-enable per project:

claude mcp add filesystem --scope project -- npx @modelcontextprotocol/server-filesystem ~/Documents

Verifying All MCP Servers

claude mcp list

Expected output:

filesystem ✓ Connected
zotero     ✓ Connected
gdrive     ✓ Connected (or paused for auth)
pubmed     ✓ Connected

The /setup-medsci skill includes this check automatically.

Common MCP Issues

Symptom Cause Fix
claude mcp list shows nothing MCP servers added at project scope but you're in a different directory Use --scope user so they persist across projects
zotero ✗ Disconnected Zotero desktop not running, or API key wrong Start Zotero, verify key at https://www.zotero.org/settings/keys
npx command not found Node.js not installed See mac.md Step 4 or windows.md Step 5
Authentication popup keeps reopening Browser blocking pop-ups Allow pop-ups for localhost

Removing an MCP Server

claude mcp remove zotero --scope user