# Zotero Paper Reader > 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. Searches Zotero when Zotero tools are available, converts PDFs to Markdown, saves to Notes/PaperInMarkdown, and provides analysis. - Skill: `fuzhiyu/zotero-paper-reader-2` (Agent Skill, multi-file: 3 files) - Install (CLI): `npx skillmds@latest add fuzhiyu/zotero-paper-reader-2` - Raw SKILL.md: https://api.skillmd.com/api/skills/fuzhiyu/zotero-paper-reader-2/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Docs & Writing - Author: fuzhiyu (https://skillmd.com/u/fuzhiyu) - Updated: 2026-09-22 - Page: https://skillmd.com/skills/fuzhiyu/zotero-paper-reader-2 --- # 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 If Zotero tools are available in the current session, use them to search for the paper: ```python # 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. If Zotero tools are not available, ask the user for one of these instead: - a Zotero attachment key - a local PDF path - enough information to locate the PDF manually in local Zotero storage ### Step 2: Get PDF Attachment Retrieve the PDF attachment information: ```python # 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: ```bash uv run python /scripts/get_zotero_pdf.py ATTACHMENT_KEY ``` Replace `` with the directory that contains this `SKILL.md`. 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 (a separate plugin) if it is installed. Explicitly invoke that skill by name and convert `PATH_TO_PDF` to `Notes/PaperInMarkdown/CLEAN_FILENAME.md`. If that skill is not installed, either: - use another local PDF-to-text workflow that preserves enough structure for the user's request, or - tell the user that the richer OCR path requires the `mistral-pdf-to-markdown` plugin **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 in sections. Since academic papers are often large (>25k tokens), read strategically: - Start with abstract and introduction (first 300-500 lines) - 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 /scripts/get_zotero_pdf.py 2HSELEHX` - Returns local path if available, or downloads and returns temp path 4. Convert: Invoke `mistral-pdf-to-markdown` skill to convert `[PDF_PATH]` → `Notes/PaperInMarkdown/Du_et_al_2023_Are_Intermediary_Constraints_Priced.md` 5. Read the Markdown file in chunks, starting with the abstract and introduction 6. Summarize and offer to dive deeper into specific sections ## Notes - The skill works with both local and web Zotero libraries - Automatic Zotero discovery requires Zotero tools in the current Codex session; otherwise the user must provide an attachment key or PDF path - 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