zotero-mineru-obsidian-paper

name

zotero-mineru-obsidian-paper

description

Ingest academic papers from Zotero into an Obsidian research knowledge base by locating the Zotero item and PDF, converting the PDF with MinerU MCP to Markdown and image assets, saving the complete conversion under raw/papers, and creating linked wiki/source notes. Use when the user asks for Zotero-to-Obsidian paper ingestion, MinerU PDF conversion, raw/papers archival, or turning a newly ingested paper into wiki knowledge notes.

Zotero MinerU Obsidian Paper

Overview

Use this skill to turn a Zotero paper into durable Obsidian knowledge: preserve the raw MinerU conversion under raw/papers, then create concise linked wiki notes from the paper.

Prefer MCP tools over ad hoc scraping. Treat Zotero metadata as the source of truth, MinerU output as the raw artifact, and Obsidian as the durable knowledge base.

Workflow

1. Locate the paper in Zotero.

   • Use Zotero MCP tools to resolve the requested library, collection path, title, and item key.
   • Read item metadata, children/attachments, notes, and available full text.
   • Record title, authors, year/date, DOI/arXiv URL, Zotero item key, attachment key, and collection path.

2. Resolve the PDF.

   • Prefer the Zotero attachment path if exposed by the MCP tool.
   • If needed, inspect the local Zotero data directory to find storage/<attachment-key>/<filename>.pdf.
   • Do not reveal private config values, API keys, signed URLs, or unrelated local paths in the final answer.

3. Find the Obsidian vault and target routes.

   • Prefer Obsidian MCP vault/file tools.
   • Respect the existing vault layout. If raw/papers and wiki exist, use them.
   • Create raw/papers/<ascii-slug>/ for the complete MinerU conversion. Use a stable ASCII slug from the paper title.
   • If the target folder already exists, inspect it and merge conservatively. Ask before overwriting user-created content.

4. Convert the PDF with MinerU MCP.

   • Use MinerU MCP parse_documents when available.
   • Use the raw paper folder as output_dir.
   • If MinerU fails on non-ASCII source or output paths, copy the PDF into the ASCII raw paper folder and parse from there.
   • Preserve the MinerU result message field verbatim for the final response.
   • If direct MinerU MCP tools are not visible but the server is installed, read references/mineru-open-mcp-fallback.md.

5. Preserve a complete raw folder.

   • Keep the original or copied PDF in the folder.
   • Keep the converted Markdown at the folder root when possible.
   • Ensure image links in Markdown resolve, usually via an images/ folder beside the Markdown.
   • Preserve useful conversion artifacts such as layout/content JSON, MCP response JSON, SDK response JSON, or extracted zip contents when available.
   • Do not store secrets or signed temporary download URLs in committed notes or final responses.

6. Convert the paper into wiki knowledge.

   • Create or update a source note under wiki/sources/.
   • Add frontmatter with bibliographic and ingestion metadata.
   • Summarize the problem, method, architecture, experiments, key results, limitations, and relevance to the user's project.
   • Create focused concept/method notes under wiki/concepts/ or wiki/methods/ for reusable ideas introduced by the paper.
   • Create or update synthesis notes under wiki/synthesis/ when the paper belongs to a broader topic such as SAR detection.
   • Use Obsidian wikilinks for concepts, datasets, methods, related papers, and project topics.

7. Verify the ingestion.

   • Count files in the raw folder and images folder.
   • Check that Markdown image references point to existing files.
   • Read back the wiki source note through Obsidian MCP.
   • Use Obsidian search to confirm that new source/synthesis content is discoverable.

Wiki Note Shape

Use this compact structure for the source note unless the vault already has a stronger convention:

---
type: paper-source
title: "Paper title"
authors:
  - "Author"
year: 2025
doi: "..."
zotero_item_key: "..."
zotero_attachment_key: "..."
raw_folder: "raw/papers/<slug>"
tags:
  - paper
  - zotero
  - mineru
---

# Paper title

## Core Claim

## Method

## Evidence

## Relevance

## Limitations

## Links

Keep concept notes short and reusable. Put paper-specific detail in the source note; put cross-paper interpretation in synthesis notes.

Final Response

Report:

• The Zotero item and attachment identified.
• The raw folder path and main Markdown path.
• The wiki notes created or updated.
• The MinerU MCP message field verbatim.
• Verification performed, including file/image counts and Obsidian search/read-back checks.

Keep the response concise and avoid exposing credentials, signed URLs, or unnecessary local configuration details.