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Paperqa MCP Server

@menyoung

代码仓库

基本信息

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其他

许可证

MIT

作者

menyoung

关于 Paperqa MCP Server

MCP server exposing PaperQA2 for deep synthesis across scientific papers

Paperqa MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

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

Paperqa MCP Server 工具

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点击上方按钮,在临时沙箱中运行此服务器并实时获取工具列表。

概览

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

常见问题

1

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.

2

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.

3

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.

4

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`.

5

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.

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