Imported from wentorai/research-plugins (skills/writing/citation/zotero-mdnotes-guide/SKILL.md). Install upstream with npx skills add wentorai/research-plugins --skill zotero-mdnotes-guide. Copyright stays with the author.

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

Key Configuration Options

Output directory: where exported Markdown files are saved
File naming convention: citation key, title, or custom pattern
Frontmatter fields: which metadata fields to include in YAML header
Annotation grouping: by color, type, page, or section
Link format: wiki-links, Markdown links, or plain text references

Frontmatter Configuration

Title, authors, year, journal, DOI are standard frontmatter fields
Tags from Zotero are converted to note tags
Custom fields can be added (read status, rating, project association)
Zotero item key is included for bidirectional linking
Date fields use ISO 8601 format for consistent sorting

Export Workflows

Single Item Export

Right-click a Zotero item and select the MDNotes export option
Choose between metadata only, annotations only, or combined export
The plugin generates the Markdown file in the configured output directory
If a file with the same name exists, choose to overwrite or create a new version
The exported file opens automatically in the configured editor (optional)

Batch Export

Select multiple items or an entire collection in Zotero
Apply export to the full selection
Each item generates its own Markdown file
A summary index file can optionally be generated listing all exported items
Batch exports respect the same templates and configuration as single exports

Annotation Export

PDF highlights are exported with their color, page number, and surrounding text
Comments attached to highlights are included as sub-items
Free-text notes from the Zotero note editor are exported as separate sections
Annotations are grouped according to the configured strategy (color, page, etc.)
Each annotation includes a link back to the specific PDF location in Zotero

Template Customization

Metadata Template

Controls the structure of the bibliographic information section
Standard fields: title, authors, year, journal, volume, pages, DOI, URL
Extended fields: abstract, keywords, collection path, date added
Custom fields: any Zotero extra field data
The template determines the order and formatting of each field

Annotation Template

Controls how individual annotations are formatted
Color mapping: assign semantic meaning to highlight colors (yellow for key findings, blue for methodology, etc.)
Include or exclude the page number, annotation date, and comment
Format as blockquotes, bullet points, or plain text
Group by color to create thematic sections automatically

Combined Template

Merges metadata and annotations into a single cohesive note
Includes section headings for clear structure
Adds a personal notes section at the bottom for your own synthesis
Includes a placeholder for connections to other notes
Provides a reading status field for tracking progress

Knowledge Management Integration

Obsidian Integration

Export to the Obsidian vault's literature notes folder
Use wiki-link format for interoperability with Obsidian's linking system
Tags are formatted as Obsidian-compatible hashtags
Dataview-compatible frontmatter enables dynamic queries
Graph view shows connections between literature notes and your other notes

Logseq Integration

Export in Logseq-compatible Markdown format
Use page references for linking between notes
Properties block replaces YAML frontmatter for Logseq compatibility
Block-level references are supported for granular linking
Journal page references connect reading dates to daily notes

Plain Markdown Workflows

Export to any directory for use with any Markdown editor
Standard Markdown formatting ensures compatibility
Frontmatter follows common conventions for static site generators
Links use standard Markdown link syntax for maximum portability
Files are self-contained with no external dependencies

Advanced Usage

Selective Field Export

Configure which Zotero fields are exported to reduce noise
Create focused templates for different project needs
Academic fields: include abstract, methodology tags, dataset references
Reading group fields: include discussion questions, presenter notes
Writing project fields: include relevance score, key quotes, argument position

Incremental Updates

Re-export items after adding new annotations
The plugin can append new annotations or regenerate the full file
Track changes between exports using version control
Maintain a changelog of reading progress through dated annotations
Sync exported files across devices using standard file sync tools

Custom Post-Processing

Apply regex transformations to exported files
Add custom metadata computed from Zotero fields
Generate index files grouping exports by tag, year, or author
Create citation graph files from the exported reference data
Format exports for specific publishing pipelines

Integration with Research-Claw

This skill connects with the Research-Claw knowledge management workflow:

Export Zotero annotations as the first step in building literature reviews
Feed exported notes to synthesis and writing skills
Connect with other citation skills for a complete reference workflow
Use exported metadata for bibliometric analysis
Store exported notes in the Research-Claw knowledge base for agent access

Best Practices

Establish your template before exporting in bulk to avoid reformatting later
Use a consistent color scheme for annotations across all papers
Export promptly after reading to capture your fresh understanding
Include a personal synthesis section in each literature note beyond just annotations
Use tags consistently to enable useful filtering and grouping
Back up both Zotero and the exported notes directory regularly

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