Zotero Color-Coded Annotation System
A systematic approach to PDF annotation in Zotero using consistent color coding to signal different types of content. This creates visual patterns that make re-reading and review more efficient.
The Color Palette
🟨 Yellow - Key Claims and Findings
Use for: Main contributions, important results, novel insights, central arguments
Example:
“Our model achieves 95% accuracy, outperforming all baselines”
Why yellow: Represents “gold” - the valuable findings you came for
🟦 Blue - Methods and Technical Details
Use for: Architecture descriptions, algorithms, experimental setup, implementation details
Example:
“We use a 12-layer transformer with 768-dimensional embeddings”
Why blue: Cool/analytical - the technical machinery
🟩 Green - Supporting Evidence and Agreement
Use for: Claims you agree with, convincing evidence, well-reasoned arguments
Example:
“Prior work shows that larger datasets improve generalization (Smith et al., 2023)”
Why green: Positive signal - this checks out
🟥 Red - Questionable Claims and Limitations
Use for: Dubious assumptions, weak arguments, acknowledged limitations, things you disagree with
Example:
“We assume the data is i.i.d. distributed”
Why red: Warning flag - investigate this
🟪 Purple - Definitions and Foundational Concepts
Use for: Terminology definitions, background concepts, domain-specific jargon
Example:
“Self-attention allows each position to attend to all positions in the previous layer”
Why purple: Foundation layer - essential for understanding the rest
Annotation Pattern
For each highlight, add a note following this structure:
[HIGHLIGHTED TEXT]
→ Interpretation: [Restate in your own words]
→ Connection: [Link to other concepts/papers]
→ Question: [What remains unclear or questionable]
→ Action: [How to use this in discussion/work]Example Annotated Passage
Text (highlighted yellow):
“Our approach reduces training time by 40% compared to baseline methods”
Note:
→ Interpretation: Significant efficiency gain through their novel optimization
→ Connection: Similar to [[Efficient Transformers]] paper's speedup claims
→ Question: What's the memory usage tradeoff? Not mentioned here
→ Action: Compare this claim with baseline paper's reported times - verify
Review Workflow
When preparing for discussion or writing:
- Filter by color in Zotero annotations panel
- Extract yellow highlights → Main points for summary
- Review red highlights → Critical analysis and limitations
- Check blue highlights → Understand methodology for questions
Why This System Works
- Consistent semantics - Same color always means same thing
- Visual scanning - Quickly find relevant content by color
- Forces categorization - Thinking about “what type” of content deepens processing
- Exportable - Color-coded annotations export to notes preserving meaning
Integration with Zettelkasten
After reading:
- Yellow highlights → Become key points in literature note
- Red highlights → Feed into critical analysis section
- Purple highlights → May spawn atomic concept notes
- Blue highlights → Technical details for reference
Related Concepts
- Research Paper Reading and Discussion Workflow - Complete reading system
- Zettelkasten Method - How to process annotations into permanent notes
- Progressive Summarization - Similar color-coding concept by Tiago Forte
Meta: This is a tool-specific workflow note for Zotero. The color system can be adapted to any PDF annotation tool, but semantics should remain consistent once chosen.