Zotero MDNotes Guide

A skill for exporting Zotero items, annotations, and notes to structured Markdown files for use in knowledge management systems like Obsidian, Logseq, or plain Markdown workflows. Based on zotero-mdnotes (1K stars), this skill creates a bridge between your reference library and your personal knowledge base.

Overview

Zotero is excellent for managing references and reading PDFs, but its note-taking capabilities are limited compared to dedicated knowledge management tools. MDNotes solves this by exporting Zotero data to Markdown files that can be used in any Markdown-compatible system. Each exported file contains bibliographic metadata, your annotations, and your notes in a structured, interlinked format.

This approach gives researchers the best of both worlds: Zotero's powerful reference management with the flexibility and interconnection capabilities of Markdown-based knowledge systems.

Configuration

Template System

• MDNotes uses Nunjucks-based templates to control the output format
• Default templates produce well-structured Markdown with YAML frontmatter
• Templates can be customized to match your preferred note structure
• Separate templates exist for item metadata, annotations, and combined notes
• Template variables provide access to all Zotero metadata fields