Section 20: Obsidian for Smart Notes

A practical system for building, connecting, and maintaining understanding


In Sections 18 and 19, we focused on how understanding is built and how ideas mature over time.

This section is about infrastructure.

Smart Notes need a place to live. That place must make it easy to capture ideas, connect them meaningfully, and return to them under pressure. If the system adds friction, students stop using it. If it demands constant organization, it collapses during busy weeks.

This section explains how to use Obsidian as a working knowledge system, not a storage tool.


What Obsidian actually is

Obsidian is a local note-taking application that stores notes as plain text files on your computer. Each note is a simple markdown document. There is no proprietary format, no required internet connection, and no forced structure.

This matters because it means:

  • your notes are durable
  • your system is not locked into a platform
  • structure can emerge gradually through use

Obsidian does not tell you how to think. It simply provides a space where connections between ideas can form naturally.

It is not:

  • a task manager
  • a document archive
  • a flashcard system
  • a productivity dashboard

Trying to make it do those things usually breaks the learning system.


Getting started: installing Obsidian and creating your first vault

This is the only setup you need to do before writing notes.

Getting Started: Installing Obsidian and Creating Your First Vault

Step 1: Download Obsidian

Download Obsidian from obsidian.md. Use the desktop version for your operating system.

Step 2: Create a new vault

  1. Open Obsidian
  2. Select Create new vault
  3. Name it something simple, such as Paramedicine Notes
  4. Choose a location on your computer you will not frequently move or rename

A vault is simply a folder on your computer. Every note you write is stored there as a plain text file.

Step 3: Ignore most settings

Do not change themes, install plugins, or adjust advanced settings. The goal is to start writing, not configuring.

Step 4: Create three folders

  • Inbox
  • Notes
  • Reference

That is enough structure to begin.


Core principle of the system

Everything that follows depends on one rule:

One note represents one idea that can stand on its own.

If notes contain multiple ideas, they cannot link cleanly.
If notes become summaries, they cannot support thinking.

Obsidian works when notes are small, explicit, and connected.


The three working spaces in your vault

Inbox

The Inbox is for capture only.

This is where:

  • lecture notes
  • scenario observations
  • questions
  • partial thoughts

go immediately, without cleanup or formatting.

Nothing stays in Inbox permanently.


Notes

This is where thinking happens.

The Notes folder contains:

  • Smart Notes (stable understanding)
  • Working notes (ideas still forming)

These are not separated by folders. They are separated by clarity.


Reference

Reference holds material you look up but do not think with directly:

  • PDFs
  • copied directive text
  • tables
  • lecture slides

Reference supports notes. It does not replace them.


How ideas move through the system

Ideas follow a consistent path.

1. Capture

You write quickly and incompletely.

Example capture notes:

  • “Patient confused before sats changed”
  • “Instructor emphasized reassessment again”
  • “Why does shock feel subtle early?”

No structure. No polish.


2. Processing

During scheduled processing sessions, you take one captured idea and ask:

  • What is this actually about?
  • What decision does it affect?
  • What mistake does it prevent?

This produces a working note.


3. Stabilization

When the idea becomes clear enough to reuse, it becomes a Smart Note.

A Smart Note:

  • explains one idea in your own words
  • stands on its own
  • links to related ideas

This is where understanding becomes reusable.


Worked example: from scenario moment to Smart Note

Worked Example: Turning a Scenario Moment into a Smart Note

Scenario moment:

During a respiratory scenario, the patient became increasingly confused before oxygen saturation changed significantly.

Capture note (Inbox):

  • Patient more confused than expected
  • Vitals didn’t look dramatic yet
  • Mental status emphasized again

Processing questions:

  • Why does cognition change early?
  • What does this prevent me from missing?
  • How would this show up in a real call?

Smart Note title:

Early hypoxia presents cognitively before it presents numerically

Smart Note content (excerpt):

Early hypoxia often presents as agitation or confusion before oxygen saturation drops significantly. Cerebral oxygen delivery is sensitive to small changes, making mental status an early warning sign. Waiting for dramatic vital sign changes delays recognition and treatment.

Links added:

  • [[Altered mental status as an early warning sign]]
  • [[Vital signs lag behind physiology]]
  • [[Reassessment timing in unstable patients]]

How to name notes so they remain usable

Titles should communicate meaning, not topic.

Good titles:

  • state a claim
  • signal a decision
  • highlight a distinction

Examples:

  • “Early shock shows up cognitively before hypotension”
  • “Task fixation often follows early intervention”
  • “Risk assessment matters more than certainty in chest pain”

If a title could be a textbook chapter, it is too vague.


Linking as reasoning, not organization

Links represent relationships that matter.

Link when:

  • two ideas influence the same decision
  • misunderstanding one breaks the other
  • they frequently appear together in scenarios

Do not link simply because topics overlap.

Links should change how you think.


Quick walkthrough: creating and linking a Smart Note

Quick Walkthrough: Creating and Linking a Smart Note
  1. Create a new note in the Notes folder
  2. Write a title that states a claim
  3. Explain the idea in full sentences
  4. Add at least one clinical implication
  5. Use [[double brackets]] to link related ideas

Only create a new linked note if the idea can stand on its own.


Weekly rhythm that keeps the system alive

Example: What This Looks Like in a Typical Week

During the week:

  • Capture quick notes during lectures, labs, and scenarios
  • Do not organize or polish

Twice per week (30–45 minutes):

  • Open Inbox
  • Select one captured idea
  • Convert it into a Smart Note or working note
  • Add 2–3 meaningful links

Before scenarios or exams:

  • Open one relevant Smart Note
  • Follow links for 5–10 minutes
  • Stop once reasoning feels activated

What to avoid early

Avoid:

  • complex templates
  • dashboards
  • heavy plugin use
  • aesthetic customization
  • turning Obsidian into a task manager

These add overhead without improving understanding.


When to change the system

Change the system only when:

  • notes no longer help you think
  • finding ideas requires constant searching
  • writing feels burdensome
  • links feel noisy instead of helpful

System changes should follow learning needs, not discomfort with imperfection.


What success looks like

A working Obsidian system:

  • grows slowly
  • feels incomplete
  • makes future learning easier
  • improves reasoning speed over time

If the system demands attention instead of supporting it, simplify.


Moving forward

At this point, you have a complete system for building and maintaining understanding.

The next step is learning how to strengthen access to the most time-sensitive parts of that understanding so it shows up reliably under pressure.

Next: Section 21: Anki for Clinical Recall