On Note Taking · Brent Anderson

When it comes to note taking, I’ve swung from “try and do all the things” to “less is more”. Altogether, there are three rules I have for myself when it comes to choosing & using tools for note taking:

Make it fun: It must be fun, or else why bother?
Make it mine: Everything should run locally with credible export. This means I control the data, where it goes, who gets to see it, and without having to put it on a server somewhere.
Make it publishable: Getting stuff out must be as easy as putting stuff in. This means I need to be able to publish to a printed book, a blog, or just peruse the notes myself.

That last point is worth savoring for a minute, as so many of these tools can feel addictive and productive, but if you’re not able to get information or value out of your notes later on, then why bother?

“One of the most basic presuppositions of communication, is that the partners can mutually surprise each other.”
Niklas Luhmann

Being able to interrogate my notes in a variety of ways is a big part of “getting stuff out”. Not only do I want to have resources I can draw on at a moment’s notice without having to interrupt my flow state, but I also want to be able to surprise myself by resurfacing things I may have thought lost to the past. Talking a random walk through my notes can spark just that sort of wonder.

My Goals

I started taking notes because I read and listen to a lot of material. I love to learn, but I found myself forgetting things pretty quickly. What’s the use of reading something if you can’t recall the best parts about it?

I have also had a journaling habit for most of my life. Writing has been a great benefit to my mental health, if only as an outlet or scratch pad for what I’ve been experiencing. It’s a wonderful thing to sit down and enter a flow state when you’re creating something - even if that something is a collection of notes that is for your own learning & growth.

Finally, I have long wanted to collect my journals, structured notes, and learnings from each year in a bound book on my shelf, perhaps if only for my own vanity. There’s something very satisfying to me about getting it all in a physical object for my shelf that I can thumb through to get a feel for how I’ve developed over time.

In a nutshell:

I want to remember what I read & listen to
I want a structured outlet for creating written content, even if it’s just for me
I want a way I can organize that note taking into publishing: both online and in print

These goals combine with those first three rules I have: make it fun, make it mine, and make it publishable. From there, we can look at the tools I’ve chosen and how I use them.

Obsidian

I use Obsidian with a pretty minimalist plugin setup. I don’t use Obsidian Sync or Publish, although perhaps I should pay them for something, as Obsidian is a pretty great tool.

My plugins:

Templater to automatically fill in my journal entry template
Update time on edit to automatically update the front matter in each of my notes
Dendron Tree to better visualize my notes. This one is pretty optional, though.

How I write with Obsidian

I only have three folders in my Obsidian vault:

Assets, where I store images and other non-note files according to the date added
Templates, where I store the raw template files for my notes
Scripts, where I have a few scripts for handling backups and some templating nonsense that others probably handle better than I do

Otherwise, every note is just a plain file in a single folder. I’ve found that folders tend to slow me down.

Instead, I record each of my notes with a naming scheme like this:

models.biology.cooperation
virtues.persuasion.aristotles-rhetorical-proofs.ethos

I’ve found that this approach is infinitely better than using folders or eschewing any naming scheme at all - and that’s after trying both of those approaches and finding them fall flat.

This is because we need to optimize for a few things in our note taking process:

Easy to capture notes: I shouldn’t have to think too hard about where something goes. Messing around with creating folders and moving things around is just too much work.
Easy to find notes: I still need a hierarchy to cluster related ideas together, and using dotted notation like this works incredibly well. The Dendron Tree plugin interprets the the dots accordingly, making it easy to still view all the files as though they are in folders if I ever want to view the notes that way. Generally I don’t, but it’s still there if I need it.
Easy to move things around: Notes will need to be moved over and over again as the system evolves. By cutting folders out of the picture completely, file renames can become pretty simple operations. At the very least, I don’t have to worry about folders existing before creating or moving a note - it’s just a simple rename.
Notes are naturally going to organize into trees and webs. We benefit from having a system that supports both, while also being easy to move things around later on.

Linking

From there, I use WikiLinks that look like this: [[models.biology.cooperation|This is a link to something about cooperation]] to link between notes. It’s a bit more tedious when first writing it out, but from there I know that these links will remain stable between my notes, with the label on each link making sense regardless of where or how I may rename each note. Obsidian will handle fixing any broken links from there, so I basically get the benefit of well-named notes and the flexibility of putting them wherever it makes sense.

Embeds

Embedding content (aka “transclusion”) between notes is one of Obsidian’s super powers, and one of the things I knew I wanted in any note taking system. Obsidian extends Markdown’s link syntax to support embeds. If I have two notes, note-a.md and note-b.md and I want to put something from A into B, I have a couple of options:

I can just copy and paste (duplication can be a good thing sometimes)
I can embed all of A into B using the syntax ![[note-b]] - the leading ! takes the entire note and embeds it in the current note
I can embed a block from A into B using the syntax ![[note-b#^block-id]]

This also works as a form of backlinking, so that I can see which bits are getting quoted & copied throughout my notes.

A word about backlinks and the graph view

I don’t tend to check these very often, but it can be helpful when exploring connections between topics. I can’t say that the graph view is interesting other than as a way to randomly drop into some part of your notes, or to view the overall structure in some way. I wish that it recognized the dotted path syntax I use for my filenames better (Dendron did this very well, showing horizontal links between different notes and vertical links between chains of notes). I doubt I’ll get around to it, but I would love to build a view like that over my notes.

Journaling

One of my key entrypoints into my notes is journaling. Most days, I don’t sit down, crack my knuckles, and start writing about a given topic. Rather, I often start by pressing a keyboard shortcut ⌘+⎇+I which invokes the Templater plugin to create a new journal entry under e.g. daily.journal.2024.11.11 . The template is pretty straightforward for prompts:

How I feel today:

What virtue is on my mind today:

(I put most of what I have to say right here)

## 2024 Goals

(I put my current goals here)

## What I am most grateful for today

## People I reached today

## What mattered most today

1. -
2. -
3. -

## What went well since my last entry

## What could have been better

## What will I do differently?

I don’t generally fill out the whole thing. The bottom half usually is left empty or deleted entirely when I’m done writing, but it’s helpful if I have things to say about those points in particular.

A note about bullets/outlining

I’ve used deeply nested outlining/bullet journal tools in the past, and I think they’re great. One problem with them is that you have a hard time referring back to stuff you’ve already written in other parts of the tree. Linking between bullets gets to be a little fiddly.

By using this dotted file approach, you get the benefit of bullets (every file is logically a sub-bullet of some other thing) without the drawbacks.

One of the other benefits of eschewing folders in favor of dotted notation for note names is that I can add sub-notes to any note, including journal entries, and it makes sense. If I have read something and want to excerpt it into my journal for reference, I can just put it under daily.journal.2024.11.11.thing-i-want-to-include and then I can write about it in the main journal entry. If I want to add other notes about that thing, I can add another level of nesting: daily.journal.2024.11.11.thing-i-want-to-include.commentary-about-this-thing. It’s a surprisingly versatile way of organizing notes without the fuss of folders.

Managing assets

I previously mentioned that one of my folders is for assets. It’s one place I do rely heavily on folders. If I were to embed a picture in this post, since today is November 11, 2024, I would put that image of a duck in assets/2024/11/11/obsidian-duck.png. The name of the image here should be mildly descriptive, and mostly lacking conflicts with anything else I store in assets today.

This is helpful so that, say, if I just need a screenshot, I can call it screenshot.png and it won’t conflict with any other screenshots I’ve added to my notes. If I have a lot of screenshots on a given day, however, I can be more precise so they don’t conflict with each other.

Learning Markdown

One unsung hero of all of this is Obsidian’s markup language, Markdown. Markdown’s history is rich and quite interesting. Suffice it to say that markdown is pretty commonplace in technology, and Obsidian’s use of markdown is no accident. I’d recommend becoming familiar with it so that you can take advantage of all of its bells and whistles, as appropriate. Obsidian’s docs reference a few different technical documents about things it supports for “Obsidian-flavored markdown”. Skim through it and see what makes sense, and you’ll get the hang of most of it as you go along.

I will call out that I use footnotes a lot in my notes. I love footnotes, as they are a great way to get an extended parenthetical in without messing up the line of thinking I might be pursuing in a given paragraph. I’m sure there are other tricks that could be used, for example in building a bibliography or glossary, but for my workflow I’ve not worried too much about it. My annual book project benefits mostly from proper headings and footnotes more than anything, with a bit of support from embedding blocks of content using the ![[embedded-note.some-sub-note#^reference]] syntax.

What about tagging?

I don’t use tags really all that much. I think some systems may benefit from more rigorous tagging, but using pretty basic Markdown most places with the above adjustments has served me quite well now for a couple of years. That’s not to say it’s not worth investigating, but for me it’s not really been worth it.

Going deeper into Obsidian’s plugins for tasks, for example, is something I’ve considered. But on the whole, this is almost everything I do with Obsidian in a nutshell.

Different types of notes

Broadly, I don’t think too much about this. That said, I do find it useful to note that each note is going to be a slightly different “species” of note. You’ll find your digital garden is a healthier ecosystem if you have a mix of different types of notes. I think this is all highly contingent on your goals for note taking in the first place: if you’re trying to organize a TTRPG campaign or a house remodel, your mileage may vary. While it’s worth learning about different ways to structure and organize your notes, the best advice is “don’t overthink it”, try the stuff that seems most interesting to you, and make sure it’s not turning into a chore.

I will say that, philosophically, I view my notes very much like a garden (and, as noted, Digital Gardening is its own field in note taking). Gardens have different species of things growing at any given time, and much of the important work happens through some form of composting or taking bits and pieces of things and letting them recombine together into something rich and wholesome for new growth.

Here’s the ladder of notes as I see it, from most polished to most atomic:

Publishable drafts: These are blog posts, articles, or manuscripts that I intend to publish. The goal of your note taking system is primarily oriented around producing something like this as output. If your goal is to blog, this would be finished blog posts. If the goal is a bound book of everything from the year, then the PDF at the end of the process is what you’re looking for here.
I’ve found that this finished format almost always ends up being polished outside of obsidian. I’ve used LaTeX in the past, and I’m planning on trying out Typst this year as it looks a little more streamlined and still well-suited to my annual book.
Journal entries: Not for public consumption, but usually the starting point of extending my notes. I start by writing about my experience, and from there I often will pull in things I’ve recently read or am thinking about, organizing those bits into other notes. This often serves as base material for publishable material.
The way that I name my notes also makes it easy for me to create summary notes for months and years without too much fuss (e.g. an entry daily.journal.2024.11.11 can roll up with the rest of the month into daily.journal.2024.11 and then all the months can roll up into a summary of the year under daily.journal.2024).
Evergreen/atomic notes: I don’t generally publish these, but I find that having them on hand is helpful for assembling bigger thoughts and pieces. This is a concept straight out of Zettelkasten, and I find that it works well in harmony with other types of notes. These are often excerpted from other books or material.
Bridge notes: I often create sub notes or notes that link multiple atomic notes together. This way, atomic notes can stay focused and concise, and my commentary about multiple concepts and how they relate can come together in its own way.

The PARA method is another approach beyond Zettelkasten that I’ve heard some good things about. I can imagine it working well if you’re trying to impose some structure on your system. I find that it’s enough ceremony and prescription that it works against my first rule (“It should spark joy”) too much, but your mileage may vary. Having the flexibility to adopt and change how I think to fit the types of thinking & work I want to accomplish far outweighs sticking dogmatically to one way of thinking about note taking, but I do think there’s a benefit to either reading about or even trying any/all of these systems. That way, you can figure out what is “too much” and lean back into the systems that help you accomplish your goals best.

After all, if it’s not helping you fulfill the reason you set out to take notes in the first place, then why bother?

Conclusion

There’s always more I could go into here, whether that’s about finding your motivation for note taking or different types of notes. I think the most important thing is to keep it simple and ensure it’s sparking joy. If it’s not fun but a chore, then it’s going to be really hard to make it into a useful habit.

Work to ensure you can get information out as much as you are putting information in. Otherwise you end up with a nest of notes that you never look back at. I think having a habit of publishing in some form helps, as it requires you to consider the consumption of what you write and not just having an endless, wiki-linked scratchpad that you add to but never actually use.

For me, I think that a note taking practice has vastly improved my well-being and health overall. It can’t imagine not having something to scratch this itch.

Appendix

The following are more technical bits about how I’ve developed my process, other tools I use in my note taking efforts (along with alternatives if you don’t want to self-host a web application), and other errata.

Honorable mentions

A few other tools I’ve looked at instead of Obsidian and why I decided to not use them:

Roam research is a really cool tool. The fact that it’s on someone else’s server was a non-starter for me, but there’s a vibrant community around this tool. Notion fits in a similar bucket. I actually use and recommend Notion for work and other collaborative wiki-like projects, but prefer the long-term stability of dumb text files on my own machine. I’ll also mention Workflowy which was my go-to outlining tool in college. I paid for a subscription for years. As noted below, only having the ability to outline without being able to link, embed, and work with individual notes is a non-starter for my workflow. Your mileage may vary.
Emacs Org Mode is also a very cool tool, but it may require a CS degree in order to use effectively. I’ve tried a few times to get into it, and it’s just too opaque for my taste. Even so, its feature set overlaps enough with Obsidian that I don’t know that I’m missing too much. Computed views over my notes would be nice, but I think the Dataview plugin may accomplish the same thing.
Foam Research was the one that really kicked things off for me. It’s built on Visual Studio Code, a tool I use every day and am very fluid with as a developer. For developers and anyone familiar with using an IDE, it’s a perfect fit. Sadly, it lacked some of the more powerful features and community support of something like Obsidian. Obsidian’s community size means that someone has probably already solved your problem. This is a huge strength to Obsidian as a product.
Dendron was my last stop before getting into Obsidian. Also based on Visual Studio Code, Dendron was philosophically excellent. It introduced me to how I name notes, and was a phenomenally sharp community. Sadly, they took investor money, were unable to find a way to profitability, and have since closed up shop. Although I could continue to use Dendron, writing plugins in Dendron was underspecified and more difficult. Again, Obsidian’s features almost entirely overlap with Dendron, Obsidian is better documented, and it’s great to benefit from those tailwinds.

obsidian-export

Obsidian Export is a command line tool that I use to convert Obsidian notes with wiki links and embedded notes/transclusions into plain Markdown files for publication in Basin. It’s simple and, while not perfect, does the job pretty well.

Pandoc

Pandoc is a Swiss army knife of file conversion. I don’t use it often, but it’s fantastic for converting markdown files out of Obsidian Export into other formats like LaTeX and Typst. Those are the formats I use for building a final PDF of my notes at the end of the year. Obsidian is great for organizing my thinking and authoring, but it’s not so great for publication. You can think of Pandoc as an automated way to process all of the files for the year from Markdown into an intermediate format (LaTeX or Typst) before getting to a PDF you can send to print.

If you’ve ever wanted to convert from any text format to any other text format, you need Pandoc.

Basin

This is something I’ve built for myself. I broadly refer to my notes as my “Pensieve” (from Harry Potter). If you’re reading this on the internet, then you are interacting with Basin. It’s my personal website and blogging platform, tailored primarily to being fast, online, and extensible. I’ve iterated on Basin for a few years, and while it doesn’t do much, it’s seen a lot of experimentation behind the scenes on how to best incorporate my notes.

A more interesting example is , or the subject.

When it comes to the deeper philosophy of note taking, I’d scour some of these exemplary websites before reading anything I have to say on the subject:

Andy Matuschak’s notebook
Maggie Appleton’s marvelous essays on digital gardens
Gwern Branwen has been doing this for a long time
Mental Nodes by Anne-Laure Le Cunff
TiddlyWiki is a platform similar to Obsidian that some rave about. I’ve tried it and couldn’t get into it, but it’s worth a look if you’re finding Obsidian to not be quite there.

Git

This is de facto standard version control software for software development. I use it in my day job, and I have a lot of muscle memory around it at this point. I wouldn’t expect anyone to pick this up for their own note taking journey, but it’s worth learning if you need any of the following:

Rewind back to any moment in the history of your notes
Make a list of all the notes you’ve added, edited, or deleted this year
Offsite backup of your notes, especially if you want those notes to be available to the general public and/or they aren’t particularly sensitive
You want to have lots of people working on the same set of notes (I don’t, but Git would be awesome for this)

Git can do a lot more than that, but those are the big ones that strike me right now. Git makes it trivial for me to start building my annual book, as I can generate a list of every file that’s been added or edited this year, and then get to work on combining those files together into a rough draft manuscript.

Archiving stuff

Keeping track of source materials is its own challenge. I have a few tools that I use here. They overlap in certain ways, and complement each other in others. I think having something that fits the description of each of these is generally useful, however because I self-host stuff it may not be reasonable for you to do the same. I include a recommendation for alternatives in each section.

The gist is that I need to archive three types of information:

Stuff I want to keep forever from the internet
Books I want to keep forever in my library
Stuff I want to read in the near future, but not this minute

This is all stuff that doesn’t really fit in Obsidian, but needs a home somewhere. Here’s how I solve those problems for myself.

Archivebox

Archivebox as a self-hosted alternative to the Internet Archive. I’m looking at using the Obsidian Web Clipper for some of this, as I think having as much as possible in my notes is best for linkability and discoverability, but sometimes you just need the source material of the original web page in context. This is particularly helpful if you want to show some measure of provenance for source material - it’s one thing to clip a snippet from a page, its another thing to show that “no, really, I have a full snapshot of what this page looked like at this exact moment in time - right down to the ads on the page”.

On a basic level, use the Obsidian Web Clipper. To step it up a little, donate to and use web.archive.org and you’ll get the same result here. The downside is that the Internet Archive is not guaranteed to be online forever, so do what you can to support their important work.

Calibre

If you’re like me, you have an eReader and a lot of digital book formats: eBooks, PDFs, and Audio books to say the least. Having a way to organize and keep track of them is critical. Calibre is free & open source and well supported, so if you haven’t tried it you may find this one easier to get into than, say, self hosting Archivebox.

I don’t think an alternative is worth calling out here, as Calibre is pretty easy to get into and should “just work”. You download it and you get going. Easy enough. Just make sure your data directory is backed up so you don’t lose all your books if when your computer explodes.

Readeck

This is a read-it-later tool: it captures stuff I want to read later but don’t have time to dig into right this minute, rather than archiving a copy of something for cold storage. The point isn’t to keep something forever, but to have it around long enough to read and decide if I want to do more with it.

Having a “read it later” service like this, Wallabag, Pocket, or Instapaper is super useful for triaging any information diet.

Miscellaneous

A few tools, in no particular order, that I rely on:

RSS for getting the news. I host my own copy of FreshRSS and use NetNewsWire to collect, fetch, store, and read the news. Find a good reader for your devices of choice and use it.
1. Use some kind of RSS - seriously, it will make your life so much better for getting news & social updates. Mastodon even natively supports it, so you can follow a feed by just subscribing to an RSS feed. Reddit, most news sources, blogs, and more all support it. Skip the adds, parse the headlines, and dig in where you think you’ll benefit the most.
A pomodoro timer so I remember to take breaks, since I’m liable to lock myself into long cycles of work without even remembering to eat lunch.
Anki - I haven’t used as much as in the past, but I’m a big believer in using flash cards for getting certain types of knowledge into my working memory. I believe this is a prerequisite to exercising that knowledge into embodied knowledge or actual mastery (e.g. memorizing conjugation tables for Spanish won’t make you a Spanish speaker, but it does make it easier to form correct sentences when you’re trying to speak so that you can build the fluency you need).
Libby for reading/listening to Audiobooks from the library. I rely on this quite a bit.
A good podcasting app. I use Overcast, but find and use Podcasts to your advantage. Farnam Street is one that’s right in the heart of all of these topics.