zotero-paper-reader

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Read and analyze academic papers from Zotero library. Use when the user requests to read, access, or analyze a paper by title, author, or topic from their Zotero library. Automatically searches Zotero, converts PDFs to markdown, saves to Notes/PaperInMarkdown, and provides analysis.

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[Academic Research]

When & Why to Use This Skill

The Zotero Paper Reader is a specialized Claude skill designed to streamline academic workflows by integrating directly with Zotero libraries. It automates the end-to-end process of searching for research papers, retrieving PDF attachments from local or cloud storage, and converting them into clean, AI-readable Markdown format for deep analysis and summarization.

Use Cases

  • Literature Review Automation: Quickly locate and summarize key findings from specific papers in your Zotero library using natural language queries like 'Read the paper about neural networks by Smith'.
  • PDF to Markdown Conversion: Automatically transform complex academic PDFs into structured Markdown files, making them easier to index, search, and reference within personal knowledge bases like Obsidian or Notion.
  • Deep-Dive Section Analysis: Efficiently analyze specific parts of long research papers (e.g., methodology, results, or citations) without exceeding LLM context limits by reading the document in strategic sections.
  • Research Organization: Maintain a clean, searchable archive of your Zotero attachments in a dedicated 'PaperInMarkdown' folder with standardized naming conventions (Author_Year_Title).
namezotero-paper-reader
descriptionRead and analyze academic papers from Zotero library. Use when the user requests to read, access, or analyze a paper by title, author, or topic from their Zotero library. Automatically searches Zotero, converts PDFs to markdown, saves to Notes/PaperInMarkdown, and provides analysis.

Zotero Paper Reader

Overview

Read and analyze academic papers directly from the Zotero library. This skill handles the complete workflow from searching Zotero to converting PDFs to readable markdown format.

When to Use

Use this skill when the user requests to:

  • "Read this paper from Zotero"
  • "Find and read [paper title]"
  • "Access [author name] paper"
  • "Get the paper about [topic]"
  • "Convert [paper] from Zotero to markdown"

Workflow

Step 1: Search Zotero Library

Use the Zotero MCP tools to search for the paper:

# Search by title, author, or keywords
mcp__zotero__zotero_search_items(query="paper title or author", limit=5)

Present the search results to the user if multiple papers are found. Get the item_key from the selected paper.

Step 2: Get PDF Attachment

Retrieve the PDF attachment information:

# Get child items (attachments) for the paper
mcp__zotero__zotero_get_item_children(item_key="ITEM_KEY")

Look for the attachment with type: application/pdf and note its Key (attachment key) and Filename.

Step 3: Get PDF File (Local or Download)

Use the bundled script to get the PDF - it automatically tries local storage first, then downloads if needed:

uv run python .claude/skills/zotero-paper-reader/scripts/get_zotero_pdf.py ATTACHMENT_KEY

The script workflow:

  1. First searches local Zotero storage (~/Zotero/storage/ATTACHMENT_KEY/)
  2. If found locally, returns that path
  3. If not found locally, downloads from Zotero web library using API
  4. Retrieves original filename from Zotero metadata and downloads to /tmp/[original_filename]

Security note: The Zotero API key and library configuration are read directly from Notes/.env by the Python script and never exposed to the LLM. Required environment variables: ZOTERO_API_KEY, ZOTERO_LIBRARY_TYPE, ZOTERO_LIBRARY_ID.

Step 4: Convert to Markdown

Use the mistral-pdf-to-markdown skill to convert the PDF:

uv run python .claude/skills/mistral-pdf-to-markdown/scripts/convert_pdf_to_markdown.py \
  "PATH_TO_PDF" \
  "Notes/PaperInMarkdown/CLEAN_FILENAME.md"

Filename convention: Create a clean filename from the paper metadata:

  • Format: Author_Year_Title.md
  • Example: Du_et_al_2023_Are_Intermediary_Constraints_Priced.md
  • Replace spaces with underscores, remove special characters

Step 5: Read and Analyze

Read the converted markdown file:

# For large papers, read in sections
Read(file_path="Notes/PaperInMarkdown/FILENAME.md", offset=1, limit=500)

Since academic papers are often large (>25k tokens), read strategically:

  • Start with abstract and introduction (first 300-500 lines)
  • Use Grep to search for specific sections if needed
  • Read specific sections based on user interest

Provide the user with:

  1. Paper metadata (title, authors, publication year)
  2. Brief summary of the abstract
  3. Main findings or sections of interest
  4. Offer to read specific sections or search for particular content

Example Usage

User request: "Read the paper 'Are Intermediary Constraints Priced' from my Zotero library"

Workflow:

  1. Search: mcp__zotero__zotero_search_items(query="Are Intermediary Constraints Priced")
  2. Get attachment: mcp__zotero__zotero_get_item_children(item_key="KPRQ2DLZ")
  3. Get PDF: uv run python .claude/skills/zotero-paper-reader/scripts/get_zotero_pdf.py 2HSELEHX
    • Returns local path if available, or downloads and returns temp path
  4. Convert: uv run python .claude/skills/mistral-pdf-to-markdown/scripts/convert_pdf_to_markdown.py [PDF_PATH] Notes/PaperInMarkdown/Du_et_al_2023_Are_Intermediary_Constraints_Priced.md
  5. Read: Read(file_path="Notes/PaperInMarkdown/Du_et_al_2023_Are_Intermediary_Constraints_Priced.md", limit=500)
  6. Summarize and offer to dive deeper into specific sections

Notes

  • The skill works with both local and web Zotero libraries
  • For web libraries, requires ZOTERO_API_KEY, ZOTERO_LIBRARY_TYPE, and ZOTERO_LIBRARY_ID in Notes/.env
  • For local libraries, Zotero local API must be enabled in Zotero preferences
  • Requires Mistral API key in Notes/.env for PDF conversion
  • Converted markdown files include extracted images in images/ subfolder
  • Large papers (>40k tokens) should be read in sections to avoid context limits

Resources

scripts/

  • get_zotero_pdf.py - Unified script that tries local storage first, then downloads from web API if needed