Quartz 5

Anki Instructions

9 min read

Vault Guide + Anki Workflow

This note is the operating guide for this vault: structure, conventions, and Anki export workflow.

1) What This Vault Is

This is a medical school Obsidian vault organized by:

  • integrated courses
  • courses
  • lessons/topics

Main dashboards:

  • Welcome links to year pages, shared notes, and this guide.
  • index builds course/lesson tables with metadata-based queries.

2) Folder Map

  • All/ -> main notes (courses, lessons, guides)
  • Attachments/ -> PDFs/images and embedded assets
  • Excalidraw/ -> drawings
  • Ink/ -> pen/input exports

3) Navigation Flow

Use this order when working:

  1. Open Welcome.
  2. Jump to Year One or Year Two.
  3. Open course note.
  4. Open numbered lesson notes in All/.

4) Metadata Conventions (Important)

index and base views depend on frontmatter. Keep it consistent.

Course note template

---
type: course
code: "84286"
year: 1
semester: 2
parent: "[[Signaling Pathways in Health and Disease (I.C.)]]"
cfu: 6
---

Integrated course template

---
type: integrated_course
year: 1
semester: 2
---

Lesson/topic template

---
type: lesson
parent: "[[Course Name]]"
---

or (when both tags are used):

---
parent: "[[Course Name]]"
type:
  - topic
  - lesson
---

5) Naming Conventions

  • Lessons usually use numeric prefixes: 01 - ..., 02 - ...
  • Keep one lesson per file.
  • Keep titles aligned with lecture order/syllabus.
  • Put new academic notes in All/ unless there is a specific reason not to.

6) Writing Style Conventions

  • Use headings to reflect lecture structure.
  • Keep formulas in LaTeX ($...$, $$...$$).
  • Use callouts for high-yield points and warnings.
  • Embed source PDFs at the top when available.

7) Anki Export: Required Rules

Deck targeting

Put this as the first line before import/export:

TARGET DECK: YourDeck::Subdeck

If missing, cards may go to default deck. Do this per file.

Card style used in this vault

This vault uses callout-based cards for Obsidian_to_Anki.

Basic card

> [!anki-basic] What is the capital of Italy?
> 
> The capital is Rome!
<!--ID: 1774205297529-->

Cloze card

> [!anki-cloze]-
> 
> The capital of Italy is {1:Rome}.
> Extra: extra info but more
<!--ID: 1774205670810-->

Important:

  • Use CurlyCloze style: {1:answer}
  • Keep Extra: only for cloze extra/back info
  • Do not add <!--ID: ...--> manually; Obsidian_to_Anki generates it on sync. If a card already has one, preserve it so updates do not duplicate the card.

8) Obsidian Callout Styling for Anki

Add this snippet to your callout CSS snippet (or existing snippet file):

.callout[data-callout="anki-basic"] {
    --callout-color: 227, 195, 211;
    --callout-icon: lucide-shield-question-mark;
}
 
.callout[data-callout="anki-cloze"] {
    --callout-color: 227, 195, 211;
    --callout-icon: lucide-shield-question-mark;
}

9) Obsidian_to_Anki Regex Setup

Set custom regexes in plugin settings:

^> \[!anki-basic\][+-]? (.*)\n((?:^>.*\n?)*)
 
^> \[\!anki-cloze\].*\n((?:(?!^> ?Extra:)^>.*\n?)*)(?:^> ?Extra:\s*(.*\n?(?:^>.*\n?)*))?

In data.json (plugin config), ensure:

"CUSTOM_REGEXPS": {
      "Basic": "^> \\[!anki-basic\\] (.*)\\n((?:^>.*\\n?)*)",
      "Basic (and reversed card)": "",
      "Basic (and reversed card)+": "",
      "Basic (optional reversed card)": "",
      "Basic (type in the answer)": "",
      "Basic amino acids": "",
      "Basic+": "",
      "Cloze": "^> \\[!anki-cloze\\].*\\n((?:(?!^> ?Extra:)^>.*\\n?)*)(?:^> ?Extra:\\s*(.*\\n?(?:^>.*\\n?)*))?",
      "Cloze+": "",
      "Dictionary Entry": "",
      "Image Occlusion": "",
      "Image Occlusion Enhanced": ""
},
"custom_regexps_dict": {
      "Basic": true,
      "Cloze": true
}

10) Legacy Syntax (Still Documented)

Legacy block format that was used:

START
Basic
Front line 1
Front line 2
Back: Back content
Tags: Test
<!--ID: 1773944978522-->
END

Legacy deletion block:

DELETE:
[id]

Use callout-based cards going forward unless you intentionally need legacy behavior.

11) AI Prompt Template for Lesson Cleanup + Cards

Use this when converting raw PPT text into a cleaned study note with cards.

You are helping a medical student study. I will paste the raw text content of a PowerPoint presentation. Your task is to refactor and reformat the content - keeping the information identical - using the following formatting conventions:
 
1. Titles & hierarchy - Use proper Markdown heading levels (#, ##, ###) to reflect slide titles and subtitles.
2. LaTeX math - Render inline math with $...$ and block/display math with $$...$$.
3. SMILES structures - When chemical structures are mentioned, render them in:
   ```smiles
   [SMILES string here]
  1. Obsidian callouts - Use the most appropriate callout type:
    • [!tip], [!warning], [!example], [!quote], [!tldr], [!info], [!important]
  2. Tables - Convert comparisons/classifications to Markdown tables when useful.
  3. Mnemonics - Allowed addition; keep clearly separated from original content.
  4. Flashcards - Insert Anki-ready cards naturally after concepts:
    • Basic:

      Question

      Answer

    • Cloze:

      Anki cloze

      Sentence with {1:answer}
      Keep the cards atomic, and prefer cloze.

  5. TLDR - End with detailed bullet summary.

Rules:

  • First line must be: TARGET DECK: Default
  • Usually, do not add info not in slides if not essential, except mnemonics and flashcards.
  • Do not remove existing content.
  • Preserve original slide order.
  • If unsure, default to [!info].
  • If you put a % symbol into latex, escape it.
  • If links are present on the slide, copy them over.


### PROMPT for integration

```text
You are integrating new source material into an existing Obsidian note. Follow these rules strictly.

## PRESERVATION RULES (never violate)
- NEVER remove, alter, or reformat any internal links: [[wikilinks]], ![[embedded files]], [markdown links](path), or any ![[image.png]] / ![[file.pdf]] embeds
- NEVER restructure or rename existing headings
- NEVER remove existing content — only expand or annotate it
- NEVER change existing LaTeX, SMILES notation, or table structure

## INTEGRATION RULES
- Place new content under the most relevant existing heading
- If no heading fits, create a new one at the appropriate level
- If a concept is already covered, expand it in place rather than duplicating it
- If the new source contradicts or nuances existing content, add a [!warning] callout immediately below the relevant passage explaining the conflict
- Supplementary details from the new source go in [!note] callouts
- Clinical or practical relevance goes in [!tip] callouts
- Keep all LaTeX for equations and quantitative expressions: $...$
- Keep SMILES notation for molecular structures
- Use Markdown tables for any new comparative content

## ANKI RULES
- Append new flashcards when relevant.
- Use [!anki-basic] for factual recall
- Use [!anki-cloze] for fill-in-the-blank
- Do not duplicate cards for concepts already covered in existing Anki section

## OUTPUT
- Return the full updated note
- Do not add any commentary outside the note itself

---

## EXISTING NOTE
<existing_note>
[paste your note here]
</existing_note>

## NEW SOURCE MATERIAL
<new_source>
[paste or upload new content here]
</new_source>

Integration w Copilot

You are integrating new source material into an existing Obsidian note. Follow these rules strictly.
 
## PRESERVATION RULES (never violate)
- NEVER remove, alter, or reformat any internal links: [[wikilinks]], ![[embedded files]], [markdown links](path), or any ![[image.png]] / ![[file.pdf]] embeds
- NEVER remove existing content — only expand or annotate it
- NEVER change existing LaTeX, SMILES notation, or table structure
 
## INTEGRATION RULES
- Place new content under the most relevant existing heading
- If no heading fits, create a new one at the appropriate level
- If a concept is already covered, expand it in place rather than duplicating it
- If the new source contradicts or nuances existing content, add a [!warning] callout immediately below the relevant passage explaining the conflict
- Supplementary details from the new source go in [!note] callouts
- Clinical or practical relevance goes in [!tip] callouts
- Keep all LaTeX for equations and quantitative expressions: $...$
- Keep SMILES notation for molecular structures
- Use Markdown tables for any new comparative content
 
## ANKI RULES
- Append new flashcards when relevant.
- Use [!anki-basic] for factual recall
- Use [!anki-cloze] for fill-in-the-blank
- Do not duplicate cards for concepts already covered in existing Anki section
  Prefer atomic cloze cards.
 
## CONTENT
- You already have the existing note.
  
  New source material:
  <new_source_material>
  </new_source_material>

Prompt for adding flashcards:

**Role:** You are a medical study assistant.
 
**Task:** Analyze the existing lesson text above and generate a series of Anki-ready flashcards.
If flashcards are already present, modify only if inaccurate or if they could be worded way better.
 
**Rules:**
 
1. **Output Location:** Do not modify, reformat, or delete any of the existing lesson text. Append all new content to the very end of the file.
    
2. **Format:** > - First line of the addition: `TARGET DECK: Default`.
    
    - Use `> [!anki-basic]` for Q&A (the title is the question, the text is the answer ) and `> [!anki-cloze]` for fill-in-the-blanks (no title so newline, text is the cloze using {1:answer}).
        
3. **Content:** Focus on high-yield facts, diagnostic criteria, and drug mechanisms mentioned in the text.
    
4. **LaTeX:** Ensure all medical formulas or concentrations use inline or
    display LaTeX. Escape % symbols (e.g., `\%`).
 
 
**Constraint:** Only output the new flashcard section. Do not repeat the original lesson content. Do not add an ID at the end of the flashcards, as it's generated automatically from the plugin.
Keep the cards atomic, and prefer cloze.

Prompt for proofreading

**Role:** You are an expert medical editor.
 
**Task:** Proofread the lesson text for clarity, medical terminology accuracy, and formatting consistency.
 
**Instructions:**
 
1. **Preservation:** Keep the original slide order and all technical information identical. Do not remove content.
    
2. **Corrections:** Fix spelling errors in complex medical terms (e.g., pharmaceutical names, anatomical structures).
    
3. **Formatting Check:**
    
    - Ensure all headers (#, ##, ###) follow a logical hierarchy.
        
    - Verify that all math/units are correctly wrapped in LaTeX `$`.
        
    - Ensure Obsidian callouts (e.g., `[!important]`) are used for critical warnings or clinical pearls.
        
4. **Style:** Maintain a professional, clinical tone. If a sentence is medically ambiguous due to a typo in the raw text, clarify it while staying true to the source material.
    
 
**Output:** Provide the corrected version of the text while maintaining all original Markdown structures.

12) Quick Troubleshooting

  • Cards not showing in intended deck:
    • check first line TARGET DECK: ...
  • Duplicate cards:
    • ensure <!--ID: ...--> is preserved
  • Cloze not recognized:
    • verify {1:...} and cloze regex
  • Basic cards not recognized:
    • verify callout title line starts exactly with > [!anki-basic]

13) One-Minute Workflow

  1. Create/update lesson note in All/ with proper frontmatter.
  2. Format notes with headings, formulas, and callouts.
  3. Add TARGET DECK: ... as first line before sync.
  4. Add/update anki-basic and anki-cloze callouts.
  5. Sync with Obsidian_to_Anki.
  6. If cards duplicate or break, check IDs and regex first.

14) CSS Snippet for floating images and multicolumn:

Transclude of MCL-Multi-Column.css

Graph View

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