Zotero-Obsidian-Wiki-Bridge

End-to-end automation: from Zotero paper management to Obsidian deep-reading notes and wiki maintenance.

English | 简体中文

Overview

Zotero-Obsidian-Wiki-Bridge connects two powerful Codex skills into one seamless research workflow:

Skill	Role
DeepPaperNote	Turns a single research paper into a high-quality Obsidian deep-reading note with evidence-first analysis, figure placeholders, and structured formatting
Obsidian Wiki Maintainer	Keeps your Obsidian research wiki consistent: auto-indexes, full-text search, linting, backfill, and topic/entity page generation

Together they automate the most tedious parts of academic reading and knowledge management — so you can focus on thinking.

Workflow

 PDF / DOI / arXiv / Zotero
         │
         ▼
   DeepPaperNote
   (evidence gathering, figure planning, note writing, lint + review)
         │
         ▼
   Obsidian Vault ──► Obsidian Wiki Maintainer
                      (index update, search refresh, conflict tracking)

Quick Start

Installation

Each skill can be installed independently via Codex skill installer:

npx skills add XuanjinZhu/zotero-obsidian-wiki-bridge/deeppapernote -a codex
npx skills add XuanjinZhu/zotero-obsidian-wiki-bridge/obsidian-wiki-maintainer -a codex

Or clone the entire repository and use the scripts directly.

Prerequisites

• Python >= 3.10
• PyMuPDF (pip install PyMuPDF) — required for DeepPaperNote, optional for Wiki Maintainer
• An Obsidian vault (recommended)
• Optional: Zotero for local paper management

Generate a Paper Note

Within Codex (or any compatible agent environment), invoke DeepPaperNote:

{给我这篇论文生成深度笔记
- DOI: 10.xxxx/xxxxx

Maintain Your Wiki

After notes are written, run the maintainer:

python obsidian-wiki-maintainer/scripts/ingest_maintain.py \
  --vault /path/to/your/vault \
  --note /path/to/new/note.md

Repository Structure

zotero-obsidian-wiki-bridge/
├── README.md
├── README.zh-CN.md
├── LICENSE
├── .gitignore
├── deeppapernote/                 # Deep paper reading skill
│   ├── SKILL.md
│   ├── README.md / README.zh-CN.md
│   ├── CHANGELOG.md
│   ├── LICENSE
│   ├── pyproject.toml
│   ├── agents/openai.yaml
│   ├── assets/
│   ├── references/
│   ├── scripts/
│   └── tests/
└── obsidian-wiki-maintainer/      # Wiki maintenance skill
    ├── SKILL.md
    ├── README.md / README.zh-CN.md
    ├── CHANGELOG.md
    ├── LICENSE
    ├── pyproject.toml
    ├── agents/openai.yaml
    ├── references/
    ├── scripts/
    └── tests/

Key Features

DeepPaperNote

• Evidence-first deep reading pipeline (not a summary generator)
• Model-led understanding: mechanism breakdown, key numbers, formulas, limitations
• Placeholder-first figure strategy — preserves figure context even when extraction is partial
• Obsidian-native output: paper-specific folder, Markdown note, local images/ directory
• Zotero integration for local-library-first paper resolution
• Lint gate + final readability review before save

Obsidian Wiki Maintainer

• Schema-driven: single Research/AGENTS.md defines your entire wiki layout
• Auto-indexing: index.md, log.md, conflicts.md kept in sync
• Full-text search with raw-source fallback layer
• Lint checks: broken links, orphans, missing frontmatter, stale entries
• Backfill: migrate legacy notes into canonical directory structure
• Query filing: persist valuable search insights into topic/entity pages

Development

See each skill's own README for development setup, testing, and contribution guidelines.

• DeepPaperNote Development
• Wiki Maintainer Development

Acknowledgments

• DeepPaperNote was originally created by dingdingcar. This fork preserves the original workflow and adapts it into the unified Zotero-Obsidian-Wiki-Bridge project.
• Thanks to the Obsidian and Zotero communities for building excellent knowledge management tools.

License

MIT — see LICENSE. Each sub-skill also carries its own MIT license.