paperqa-mcp-server

Name: paperqa-mcp-server
Author: menyoung

@menyoung

Repository

About paperqa-mcp-server

MCP server exposing PaperQA2 for deep synthesis across scientific papers

Basic information

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "paperqa-mcp-server": {
      "command": "uvx",
      "args": [
        "paperqa-mcp-server",
        "index"
      ]
    }
  }
}

Tools

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Overview

What is paperqa-mcp-server?

paperqa-mcp-server gives Claude the ability to read, search, and synthesize across your entire PDF library. It is built on PaperQA2 and points at a Zotero storage folder (or any folder of PDFs), enabling deep reading and question answering across multiple papers.

How to use paperqa-mcp-server?

Install the uv package manager and obtain an OpenAI API key. Run uvx paperqa-mcp-server once to warm the cache, then configure Claude Desktop by adding a paperqa entry in claude_desktop_config.json with the full path to uvx and your API key. Pre‑build a search index with uvx paperqa-mcp-server index (required if you have more than ten unindexed papers). After restarting Claude Desktop, the paper_qa tool appears.

Key features of paperqa-mcp-server

Deep reading and synthesis across PDFs using PaperQA2
Indexes and searches an entire Zotero storage folder
Integrates natively with Claude Desktop via MCP
Uses OpenAI embeddings and LLMs for internal reasoning
Pre‑build index avoids runtime latency on large libraries
Pairs with zotero-mcp for cross‑referencing metadata

Use cases of paperqa-mcp-server

Ask Claude questions that require evidence from multiple research papers
Rapidly synthesize findings across hundreds of PDFs in Zotero
Combine with zotero-mcp to browse library metadata and annotations
Query personal PDF collections with natural language and get cited answers

FAQ from paperqa-mcp-server

Why does Claude show “Server disconnected”?

Claude Desktop has a short startup timeout. If uv needs to download packages on first launch, it will time out. Fix: run uvx paperqa-mcp-server once from the terminal first.

Why does the server say “Index incomplete” when I query?

The server checks the index before each query. If too many papers are unindexed, it returns a diagnostic message. Fix: run uvx paperqa-mcp-server index to build the full index.

The hammer icon doesn’t appear. What’s wrong?

Make sure you quit Claude Desktop completely (Cmd+Q) and reopened it. Check for JSON syntax errors in claude_desktop_config.json – a missing comma is the most common mistake.

Does paperqa-mcp-server use Claude for its internal reasoning?

No. PaperQA2 uses its own LLM (default gpt-4o-mini) for embeddings and synthesis. You can change the model via environment variables PQA_LLM, PQA_SUMMARY_LLM, and PQA_EMBEDDING.

What are the runtime requirements?

Python managed by uv, an OpenAI API key, and a folder of PDFs (default ~/Zotero/storage). The index is stored locally at ~/.pqa/indexes/. The server uses MCP stdio transport and authenticates via the OPENAI_API_KEY environment variable.