Obsidian

Obsidian is an extensible, local-first, and cross-platform Markdown editor.

Features

• Your notes are stored in Obsidian-flavored Markdown (wikilinks, YAML frontmatter, etc).
• Local-first: you have direct control over your files because they are plaintext, not some special encrypted crap like Evernote’s. Many sync options are available (Obsidian Sync - paid, Syncthing, Git, Google Cloud/iCloud, etc). See sections below for more details.
• Bidirectional linking. You can see what notes referenced the current note at a glance, which helps you form connections and navigate your vault with ease.
• Note organization: folders, hierarchical tagging
• Properties (file metadata)
• Community plugins
• iframe embeds (and HTML in general thanks to Markdown)

Organization

I mainly use a flat hierarchy to organize my notes, and I use folders only when needed (i.e., to organize distinctly different types of notes such as Literature/ or Periodic/, or to restrict access like Private/). I think folders are mostly counterproductive for a knowledge base, since searching via text, tags, and properties will always be faster than clicking through folder. I even used to put all security-related notes in their own folder called Security/ and I just found organizing to be too much of a chore, though now there are plugins that can help you move files into the correct folder automatically. If you manage projects with Obsidian then folders may actually beneficial since they help you divide your files into different contexts. I also try to avoid nesting folders and tag taxonomy as much as possible since they often introduce more overhead than benefits.

As for tags vs links, I use tags mainly for note type (e.g., literature, daily, TTP, blog post) and use links for everything else so that I could easily see all backlinks when I’m on the corresponding note; I don’t want my tag panel to explode after all. I use related and sources properties to link notes as appropriate, and I have also added relevant sections to the website using these metadata.

In addition, I use daily notes extensively to take lecture notes. In any given course note, I can see the lecture notes by glancing at the backlinks panel. If I feel the need to review for an exam, I typically follow the backlinks and convert my lecture notes into permanent notes.

Publishing Your Notes

If you want to publish your notes like me, consider using open-source solutions such as Quartz (the one I’m using), the Obsidian Digital Garden plugin (which I’ve used prior to quartz), the paid Obsidian Publish (somewhat pricey), or other static site generators. Obsidian is a handy Markdown editor in my opinion, so even if you’re not using Obsidian to take notes, you can still use it as an editor when using other Markdown-based publishing solutions.

Syncing

There are multiple free and paid solutions for syncing:

• In general, choose Syncthing, which is a cross-platform file syncing client that is blazing fast and also runs in the background to keep your files updated even when Obsidian is not open on other devices you use. You can technically use it on iOS, but Obsidian won’t be able to access whatever folder Syncthing synced due to iOS restrictions.
• If you want something that is integrated into Obsidian itself, choose Obsidian Sync (paid), which has built-in version history and is relatively configurable. See official docs. Note that Obsidian Sync only syncs when the app is open, so if you don’t open mobile Obsidian that often, it’ll take some time to sync and index your notes—you can still browse your notes in the meantime, just don’t edit anything.
• If you use Apple products, you must choose between iCloud or Obsidian Sync, both of which are paid. There may be other solutions like this one, but they are far more user unfriendly than the paid ones.
• If you are tech-savvy, you can also consider using git to sync your notes through GitHub, GitLab, or even your self-hosted git server. You can use the Obsidian Git plugin, to periodically pull, commit, and push. This works but doesn’t sync your notes in real time.

Backup

Please back up your vault. You spent countless hours in your vault and you probably don’t want to lose it, ever. Consider syncing to multiple devices, saving copies of your vault to external drives, and backing it up to other services such as GitHub, Google Drive, etc.

Plugins

Obsidian plugins extend the functionality of your editor. My favorite plugins are:

• Excalidraw (helps me make diagrams in lecture).
• BibNotes (helps me import Zotero items and annotations)
• Omnisearch (allows fast full-text search of my vault)
• Supercharged Links (I use it to color and add emojis to Obsidian links based on tags)
• Latex Suite (helps me type LaTeX quickly via snippets)
• Templater (helps me set up a new note quickly, e.g., daily notes)
• Vimrc support (a god send for adding custom Vim keybindings)
• Paste image rename (automatically renames a pasted image)
• Image Toolkit (allows me to click and enlarge an image)

A lot of people also use Dataview, but I personally haven’t found much use for it. I hope the upcoming Dynamic Views feature on the Obsidian roadmap would serve as a nice built-in replacement for Dataview and also mirror the Notion database feature.

Task Management

There are people who manage tasks using Obsidian, but personally I just find task management to be overly clunky in Obsidian even with plugins. You can try it out for yourself, but I’d consider using TickTick, Todoist, or other dedicated to-do list apps, which have a cleaner UI, third-party integration, reminders, etc. It’s just much more convenient to use something made for task management.