docs/3-USER-GUIDE/working-with-notes.md
Notes are your processed knowledge. This guide covers how to create, organize, and use them effectively.
Notes are your research output — the insights you capture from analyzing sources. They can be:
Unlike sources (which never change), notes are mutable — you edit, refine, and organize them.
1. In your notebook, go to "Notes" section
2. Click "Create New Note"
3. Give it a title: "Key insights from source X"
4. Write your content (markdown supported)
5. Click "Save"
6. Done! Note appears in your notebook
1. Have a Chat conversation
2. Get a good response from AI
3. Click "Save as Note" button under response
4. Give the note a title
5. Add any additional context
6. Click "Save"
7. Done! Note appears in your notebook
1. Go to "Transformations"
2. Select a template (or create custom)
3. Click "Apply to sources"
4. Select which sources to transform
5. Wait for processing
6. New notes automatically appear
7. Done! Each source produces one note
Title: "What you're capturing"
(Make it descriptive)
Content:
- Main points
- Your analysis
- Questions raised
- Next steps
Metadata:
- Tags: How to categorize
- Related sources: Which documents influenced this
- Date: Auto-added when created
You can format notes with markdown:
# Heading
## Subheading
### Sub-subheading
**Bold text** for emphasis
*Italic text* for secondary emphasis
- Bullet lists
- Like this
1. Numbered lists
2. Like this
> Quotes and important callouts
[Links work](https://example.com)
# Key Findings from "AI Safety Paper 2025"
## Main Argument
The paper argues that X approach is better than Y because...
## Methodology
The authors use [methodology] to test this hypothesis.
## Key Results
- Result 1: [specific finding with citation]
- Result 2: [specific finding with citation]
- Result 3: [specific finding with citation]
## Gaps & Limitations
1. The paper assumes X, which might not hold in Y scenario
2. Limited to Z population/domain
3. Future work needed on A, B, C
## My Thoughts
- This connects to previous research on...
- Potential application in...
## Next Steps
- [ ] Read the referenced paper on X
- [ ] Find similar studies on Y
- [ ] Discuss implications with team
Workflow:
Chat → Good response → "Save as Note"
→ Edit if needed → Save
When to use:
- AI response answers your question well
- You want to keep the answer for reference
- You're building a knowledge base from conversations
Quality:
- Quality = quality of your Chat question
- Better context = better responses = better notes
- Ask specific questions for useful notes
Workflow:
Ask → Comprehensive answer → "Save as Note"
→ Edit if needed → Save
When to use:
- You need a one-time comprehensive answer
- You want to save the synthesized result
- Building a knowledge base of comprehensive answers
Quality:
- System automatically found relevant sources
- Results already have citations
- Often higher quality than Chat (more thorough)
Workflow:
Define transformation → Apply to sources → Notes auto-created
→ Review & edit → Organize
Example Transformation:
Template: "Extract: main argument, methodology, key findings"
Apply to: 5 sources
Result: 5 new notes with consistent structure
When to use:
- Same extraction from many sources
- Building structured knowledge base
- Creating consistent summaries
Open Notebook comes with presets:
Summary
Extracts: Main points, key arguments, conclusions
Output: 200-300 word summary of source
Best for: Quick reference summaries
Key Concepts
Extracts: Main ideas, concepts, terminology
Output: List of concepts with explanations
Best for: Learning and terminology
Methodology
Extracts: Research approach, methods, data
Output: How the research was conducted
Best for: Academic sources, methodology review
Takeaways
Extracts: Actionable insights, recommendations
Output: What you should do with this information
Best for: Practical/business sources
1. Go to "Transformations"
2. Select a template
3. Click "Apply"
4. Select which sources (one or many)
5. Wait for processing (usually 30 seconds - 2 minutes)
6. New notes appear in your notebook
7. Edit if needed
1. Click "Create Custom Transformation"
2. Write your extraction template:
Example:
"For this academic paper, extract:
- Central research question
- Hypothesis tested
- Methodology used
- Key findings (numbered)
- Limitations acknowledged
- Recommendations for future work"
3. Click "Save Template"
4. Apply to one or many sources
5. System generates notes with consistent structure
Option 1: Date-based
2026-01-03 - Key points from X source
2026-01-04 - Comparison between A and B
Benefit: Easy to see what you did when
Option 2: Topic-based
AI Safety - Alignment approaches
AI Safety - Interpretability research
Benefit: Groups by subject matter
Option 3: Type-based
SUMMARY: Paper on X
QUESTION: What about Y?
INSIGHT: Connection between Z and W
Benefit: Easy to filter by type
Option 4: Source-based
From: Paper A - Main insights
From: Video B - Interesting implications
Benefit: Easy to trace back to sources
Best practice: Combine approaches
[Date] [Source] - [Topic] - [Type]
2026-01-03 - Paper A - AI Safety - Takeaways
Tags are labels for categorization. Add them when creating notes:
Example tags:
- "primary-research" (direct source analysis)
- "background" (supporting material)
- "methodology" (about research methods)
- "insights" (your original thinking)
- "questions" (open questions raised)
- "follow-up" (needs more work)
- "published" (ready to share/use)
Benefits of tags:
You can reference sources within notes:
# Analysis of Paper A
As shown in Paper A (see "main argument" section),
the authors argue that...
## Related Sources
- Paper B discusses similar approach
- Video C shows practical application
- My note on "Comparative analysis" has more
AI Note:
"The paper discusses machine learning"
What you might change:
"The paper proposes a supervised learning approach
to classification problems, using neural networks
with attention mechanisms (see pp. 15-18)."
How to edit:
1. Click note
2. Click "Edit"
3. Refine the content
4. Click "Save"
When saving from Chat/Ask:
- Citations auto-added
- Shows which sources informed answer
- You can verify by clicking
When manual notes:
- Add manually: "From Paper A, page 15: ..."
- Or reference: "As discussed in [source]"
Notes are fully searchable:
Find exact phrase: "attention mechanism"
Results: All notes containing that phrase
Use when: Looking for specific terms or quotes
Find concept: "How do models understand?"
Results: Notes about interpretability, mechanistic understanding, etc.
Use when: Exploring conceptually (words not exact)
Text search notes → Find keyword matches
Vector search notes → Find conceptual matches
Both work across sources + notes together
Copy to clipboard
Click "Share" → "Copy" → Paste anywhere
Good for: Sharing one note via email/chat
Export as Markdown
Click "Share" → "Export as MD" → Saves as .md file
Good for: Sharing with others, version control
Create note collection
Select multiple notes → "Export collection"
→ Creates organized markdown document
Good for: Sharing a topic overview
Publish to web
Click "Publish" → Get shareable link
Good for: Publishing publicly (if desired)
Phase 1: Discovery
Phase 2: Deep Dive
Phase 3: Synthesis
Summaries
Questions
Insights
Tasks
You can reference notes:
"Based on my note 'Key findings from A',
how does this compare to B?"
Notes become part of context.
Treated like sources but smaller/more focused.
Notes can be transformed:
1. Select notes as input
2. Apply transformation
3. Get new derived notes
Example: Transform 5 analysis notes → Create synthesis
Notes are used to create podcast content:
1. Generate podcast for notebook
2. System includes notes in content selection
3. Notes become part of episode outline
| Mistake | Problem | Solution |
|---|---|---|
| Save every Chat response | Notebook becomes cluttered with low-quality notes | Only save good responses that answer your questions |
| Don't add tags | Can't find notes later | Tag immediately when creating |
| Poor note titles | Can't remember what's in them | Use descriptive titles, include key concept |
| Never link notes together | Miss connections between ideas | Add references to related notes |
| Forget the source | Can't verify claims later | Always link back to source |
| Never edit AI notes | Keep generic AI responses | Refine for clarity and context |
| Create one giant note | Too long to be useful | Split into focused notes by subtopic |
1. CREATE
├─ Manual: Write from scratch
├─ From Chat: Save good response
├─ From Ask: Save synthesis
└─ From Transform: Batch process
2. EDIT & REFINE
├─ Improve clarity
├─ Add context
├─ Fix AI mistakes
└─ Add citations
3. ORGANIZE
├─ Name clearly
├─ Add tags
├─ Link related
└─ Categorize
4. USE
├─ Reference in Chat
├─ Transform for synthesis
├─ Export for sharing
└─ Build on with new questions
5. MAINTAIN
├─ Periodically review
├─ Update as understanding grows
├─ Archive when done
└─ Learn from organized knowledge
Your notes become your actual knowledge base. The more you invest in organizing them, the more valuable they become.