Skip to content

Claude Desktop Setup

This guide walks you through setting up Scholar MCP with Claude Desktop, from basic search to full PDF conversion.

Step 1: Basic setup

Add the server to your Claude Desktop configuration (claude_desktop_config.json):

~/Library/Application Support/Claude/claude_desktop_config.json

%APPDATA%\Claude\claude_desktop_config.json

~/.config/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "scholar": {
      "command": "uvx",
      "args": ["--from", "pvliesdonk-scholar-mcp", "scholar-mcp", "serve"],
      "env": {}
    }
  }
}

Restart Claude Desktop. You should see the Scholar MCP tools in the tool list.

Note

Without an API key, Semantic Scholar limits you to ~1 request per second. This works fine for occasional lookups but may feel slow during multi-step explorations.

Step 2: Add an API key

Request a Semantic Scholar API key (free, approval usually takes a few days).

{
  "mcpServers": {
    "scholar": {
      "command": "uvx",
      "args": ["--from", "pvliesdonk-scholar-mcp", "scholar-mcp", "serve"],
      "env": {
        "SCHOLAR_MCP_S2_API_KEY": "your-key-here"
      }
    }
  }
}

This bumps the rate limit to ~10 req/s, making graph traversals and batch operations much faster.

Step 3: Enable PDF conversion

To download and convert open-access PDFs, you need:

  1. A running docling-serve instance
  2. Write mode enabled (READ_ONLY=false)

Start docling-serve:

docker run -p 5001:5001 ghcr.io/ds4sd/docling-serve:latest

Update your config:

{
  "mcpServers": {
    "scholar": {
      "command": "uvx",
      "args": ["--from", "pvliesdonk-scholar-mcp", "scholar-mcp", "serve"],
      "env": {
        "SCHOLAR_MCP_S2_API_KEY": "your-key-here",
        "SCHOLAR_MCP_DOCLING_URL": "http://localhost:5001",
        "SCHOLAR_MCP_READ_ONLY": "false",
        "SCHOLAR_MCP_CACHE_DIR": "/tmp/scholar-mcp"
      }
    }
  }
}

Cache directory

When running locally, set SCHOLAR_MCP_CACHE_DIR to a writable directory like /tmp/scholar-mcp or ~/.local/share/scholar-mcp. The default (/data/scholar-mcp) is designed for Docker.

Step 4: Add OpenAlex polite pool

Set your contact email to get faster OpenAlex rate limits:

{
  "mcpServers": {
    "scholar": {
      "command": "uvx",
      "args": ["--from", "pvliesdonk-scholar-mcp", "scholar-mcp", "serve"],
      "env": {
        "SCHOLAR_MCP_S2_API_KEY": "your-key-here",
        "SCHOLAR_MCP_DOCLING_URL": "http://localhost:5001",
        "SCHOLAR_MCP_READ_ONLY": "false",
        "SCHOLAR_MCP_CACHE_DIR": "/tmp/scholar-mcp",
        "SCHOLAR_MCP_CONTACT_EMAIL": "you@example.com"
      }
    }
  }
}

Example prompts

Once configured, try asking Claude:

  • "Search for recent papers on retrieval-augmented generation published after 2023"
  • "Get the citation graph for this paper: DOI:10.48550/arXiv.2005.11401 with depth 2"
  • "Find a bridge paper connecting attention mechanisms and graph neural networks"
  • "Enrich this paper with OpenAlex data: DOI:10.1038/s41586-021-03819-2"
  • "Download and convert the PDF for arXiv:2005.11401 to Markdown" (requires Step 3)