Taking notes with Obsidian

A color photo showing several worn notebooks stacked on top of each other.

For a few years now, I’ve been using Obsidian to keep a daily journal, and it’s been great. It has a lot of options that I’ve never explored or needed but something came up recently and I wanted to find out how to connect Obsidian to Zotero. An online search using DuckDuckGo returned an unexpected result. One of the first results was about using Obsidian as Zettelkasten, which is something I’d never heard about. I fell down the rabbit hole and my mind was blown.


The first question that came to mind was “What’s a Zettelkasten?” I’d never heard of the term before, so it was a new concept to me. An oversimplified description would be that it’s a method of taking and filing notes that leads to greater understanding of their contents.

According to the blog post, Zettelkasten was devised German sociologist and philosopher Niklas Luhmann. He needed a system to help him collect and organize his notes, and what he developed was Zettelkasten. In English, the word is usually translated as “slip box”, but personally I think of it as a card catalog since it looks like he wrote his notes on index cards and put them into card cabinets. The idea that notes can be systematically organized was an epiphany for me. I realized I’ve been doing notes all wrong.

My days in grade school pre-date the internet. Even my first few attempts at college were before the internet became a thing. I don’t recall any classes on study skills, or anyone explaining much about it other than saying, “find what works for you.” I couldn’t turn to YouTube, Wikipedia, or anywhere else for tips on study skills and note taking, so “what works” for me wound up as a collection of disorganized habits that sometimes worked and sometimes didn’t.

The blog post mentioned above discussed different types of notes, which is also something I hadn’t really considered, but immediately understood. The author mentions literature notes, fleeting notes, and permanent notes, but then explains he doesn’t use literature notes that often, so he concentrated on the other two.

A color photo showing dozens of sticky notes arranged on a bulletin board.
Fleeting notes in action.
Fleeting notes are meant to be short-lived and can be discarded not long after being created. I liken these to the sticky notes I write in my office and post on my monitor or above my desk. Looking at them now, I see some that are reminders for things I did or meant to do several months ago, others are reminders to do things I’m still procrastinating on, and still others are a collection of chengyu (Chinese proverbs) from a former colleague. While most of these notes are fleeting, I plan to convert the latter ones to permanent notes.

Permanent notes are ones that are meant to be kept because the information they contain will be useful for a long time. Creating permanent notes is almost like foreshadowing in real life, because it’s information that will be useful in the future.

From my understanding, a work habit to get into is to review fleeting notes on a daily or weekly basis. If they’re not worth keeping, get rid of them. If they have information that will be needed in the future, they should be turned into permanent notes. This is done by giving them more context, adding to their content, or otherwise making them more useful so they can be easily understood when reviewed in the future.

While the post on using Obsidian as Zettelkasten was interesting, it was only the start of my fall down the rabbit hole because it linked to another blog post that described Maps of Content, otherwise known as MOCs.

Maps of Content

Since finding out about Maps of Content, I’ve created over a hundred notes and organized them into multiple MOCs. A MOC is a note that links to multiple other notes on a certain topic, but those notes also connect back to the MOC. Let me provide an example.

I’m in grad school and taking a couple of classes. Each class has material the students are supposed to read and discuss. I started by creating the following MOC notes for each class in Obsidian:

  • EDUC-J501 MOC
  • EDUC-R541 MOC

I began each of those notes with the following snippet code, which collects all links to the note into an unordered list.

list from [[]] and !outgoing([[]])

In the EDUC-J501 class, a recent assignment was to read Color-blind Racism in Pandemic Times (Bonilla-Silva, 2020), so I created a note in Obsidian with the name of the article as the title. At the top of the note I added [[DEI MOC]] and [[EDUC-J501 MOC]], because while I took notes on the article in relation to the class, I also wanted to collect notes on a similar topic in a MOC for Diversity, Equity, and Inclusion, commonly known as DEI.

After I began playing with MOCs, it transformed how I take notes and I got a bit carried away with it over the weekend. What follows below are the steps that helped me finally get organized in note taking.

Plugins and color-coding

A screenshot showing the the Zotero Integration plugin is installed in Obsidian.
Zotero Integration plugin
To really get organized I had to add a few Community Plugins to Obsidian. As mentioned at the start of the post, I was looking for a way to connect Obsidian to Zotero, and the way to do that is with the Zotero Integration plugin. In addition to installing and enabling this plugin in Obsidian, I also had to download and install the Better BibTeX plugin for Zotero. After both were working, it became much easier to add citations and bibliographies from Zotero into Obsidian.

Great! That’s what you set out to do in the first place. You’re done, right?

Nope. This is just scratching the surface.

The snippet of code at the top of each MOC note requires a plugin known as Dataview. I have a feeling there is a lot more to the Dataview plugin that I’ll have to look into, but for the moment I’m happy with it collecting the links.

The next plugin I installed is known as File Color and it may have more impact on my note taking than the plugins mentioned above. This is because it gives me the ability to color-code the names of the files. Why is this important? Because I can tell at a glance if something is a MOC or a regular note. I can tell blog posts from blog drafts, and notes on articles from notes on books. When the list of notes grows to a few hundred or a few thousand, being able to quickly tell the differences between the different types of notes will probably come in handy.

A screenshot of the options for the File Color plugin for Obsidian. The options show several color codes to represent different groups.
An example of some color codes created in the File Color plugin in Obsidian.

With the color codes, it would be easy to come up with dozens of different colors to represent different ideas. Too easy. Since the plugin only changes the color of the file name in the Obsidian sidebar, if there were too many colors, it would become difficult to distinguish them from one another. Because of that, I purposefully limited the number of colors I’m using for now. If the need comes up in the future, more can be added.

As it stands now, most of the files in my notebook are blue because they are in the People, places, things, concepts group. Though it wasn’t intended that way, it’s become a bit of a catchall. As the collection of notes grows, I will probably break it into separate groups.

MOC example 1: Second Life and Virtual Worlds

Rather than just describing my new, and still evolving, note-taking habits, I thought it would be a good idea to give a few examples of it in practice. Most of the notes I created over the weekend have to do with Second Life, and I think of them as practice for using Maps of Content in addition to their usefulness in a subject that interests me.

For the purposes of this tutorial, I created a new vault so we can start with something new and organize it as we go along. One shortcoming of using Obsidian as Zettelkasten or with Maps of Content is that the links don’t work across different vaults. Most people will probably only need one vault, but if they want to use more than one, they should know this limitation.

A screenshot of an empty vault in Obsidian.
An empty vault in Obsidian.

Maps of Content are ultimately about organizing content, so let’s start by creating a note. In Obsidian, I started a new note and titled it Michael Voxel after the name of my Second Life avatar. At this point the content is very simple, as seen below, but I can expand on it later.

[[Second Life MOC]]

**Michael Voxel** is a resident of [[Second Life]]. He likes photography, exploring the grid, and hanging out in cafés.

Simple, and a good place to start taking notes. Obsidian uses Markdown, which is a language used for structuring documents. In the section above, [[Second Life MOC]] and [[Second Life]] create links to other notes in the vault, even if they haven’t been created yet. The asterisks in **Michael Voxel** simply makes the text bold and is similar to the <b></b> tags in HTML.

I clicked on the [[Second Life]] link to create another note, with the content below:

[[Second Life MOC]]

**Second Life** is a [[Virtual world|virtual world]] created by [[Linden Labs]].

In the note above, [[Virtual world|virtual world]] links to a note titled Virtual world, but shows up in this note as virtual world. This is mainly an issue with English grammar and how words are capitalized. Anything before the | will be the name of the note that is being linked, while anything after the | will be what shows up in the note being edited. It took a little getting used to, but it works for me.

After creating notes for Virtual world and Linden Labs, I turned my attention to the Second Life MOC note. As mentioned earlier, the code for this file is just:

list from [[]] and !outgoing([[]])

At this point, if the Dataview plugin is doing its job, the Second Life MOC note shows up as something like the following:

  • Linden Labs
  • Virtual world
  • Second Life
  • Michael Voxel

As Miller pointed out in Quickly Organize Notes in Obsidian, this list isn’t very useful in its current form and it’s better to treat it as a to do list of notes that still need to be organized. After organizing the note, it looks something like this:

list from [[]] and !outgoing([[]])
## People
+ [[Michael Voxel]]

## Organizations
+ [[Linden Labs]]
+ [[Second Life]]

## Concepts
+ [[Virtual world]]

When a link is added elsewhere in a note, it automatically disappears from the dataview section. In Markdown, the pound sign (#) is used for headings so ## People shows up as a second-level heading. Unordered lists can be created by using a plus sign (+), as in the case of + [[Michael Voxel]] and the others.

A screenshot showing color-coded file names in Obsidian.
Color-coded file names in Obsidian.
With the Map of Content started, it’s a good time to start color-coding the file names. Since there are only a few notes, and this vault is just an example, only a couple of colors are being used, as seen in the image on the left. Second Life MOC is sort of a goldenrod yellow which I use to distinguish Maps of Content, while the rest of the notes are blue because they represent People, places, things, concepts.

In this example, I showed how to create a simple Map of Content in Obsidian with the help of a few plugins. It expands on the work described in the blogs posts on the Obsidian website, but it’s still only scratching the surface. In the next example, I show how to use the Zotero Integration plugin and start taking notes on books and articles.

MOC example 2: Books, articles, and Zotero

In addition to using MOCs to create simple notes as shown in the previous example, they’re also an excellent way to organize long form notes on literature such as books and articles. For me, this is where the Zotero Integration Plugin is really useful. I’ll discuss taking notes on books and articles in a bit, but first I want to go over setting up the Zotero Integration Plugin as well as the Highlightr plugin.

A screenshot showing the citation format settings in the Zotero Integration Plugin in Obsidian.
Citation format settings in the Zotero Integration Plugin.
For the Zotero Integration Plugin to work well, it’s necessary to setup a couple of citation styles, as seen in the image at right. One of the styles is for bibliography entries while the other is for in-line citations.

I’m working on a master’s degree in Education and the preferred citation style in this field is APA. The plugin has several different styles to choose from, so I chose “American Psychological Association 7th edition” as the Citation Style for both. It’s also a good idea to give each a more descriptive name so it’s easier to find when it’s used later.

After setting up the Zotero Integration Plugin, I also recommend installing the Highlightr plugin. For my purposes the default settings for that are fine, but it’s nice to know there’s the ability to add more colors or choose the highlighting style. In the book note example below, both plugins have been used.

A screenshot of the beginning of a note I'm creating while I read the book Ethnography and Virtual Worlds.
An example of a book note.

There’s a lot going on in the image above, so let take a few moments to describe it. In the menu showing the titles of the notes, it shows many more notes have been added, and as shown by the variety of colors, there are more note types as well.

This particular note is for the book Ethnography and Virtual Worlds (Boellstorff et al., 2012), which is related to my interest in Second Life. At the top of the note, I created links for the MOCs I want this note to appear in. Since the book is mainly about anthropology methods in virtual worlds, I thought it might be a good idea to start MOCs for anthropology and virtual worlds since I suspect I’ll be reading more works on those topics in the future.

Underneath those links, I added a bibliographic reference for the book itself. I’m not sure if I’ll ever need it, but it’s reassuring to know it’s there. Following this is a second-level heading titled “Foreword” to show the part of the book being referenced. Each chapter gets its own heading, and at the very bottom of the screenshot, it’s possible to see the heading for “Chapter 1”.

The Foreword of the book starts with a quotation and I treat these a little different than the rest of the notes. Just before the quote, I type in #quotation.

When a # is followed by a space, Obsidian creates a heading, but when there isn’t a space, it creates a hashtag.

When an author puts a quotation in a book or article, if it seems interesting, I like to put it in my notes. To make them easier to find, I use the #quotation hashtag. It’s very rare I do searches in Obsidian, but when I do, I’m usually looking for a quotation and the hashtag has a chance to do it’s job. Chris Bowler has a good post about how Obsidian uses hashtags and it’s worth a quick read.

Following the hashtag, and to make the quote more distinctive among the rest of the notes, I start with a >. In Markdown, this is used for quotation blocks and it indents the text and adds a purple line to left, setting the block apart from the rest of the text. At the end of the quote, I put the original source. This would normally be the author, but in this case it is a book written by a committee, so I put the title of that book instead.

At the end of the quote and at the end of every note, I put the page number in parentheses. Since this quote is part of the Foreword and not the regular text, it has some Roman numerals instead of the usual Arabic ones. Putting the page number will help me if I’m reviewing my notes and want to go back to the original source to get more context.

I’m not sure if other people take notes the same way I do, but when I’m reading a book or article and find a section that’s interesting I highlight the original text, then copy the highlighted section to my notes. If the book is in physical form, as this one is, it means I have to type it in. I’m not great at typing, but I usually manage to muddle through. If the book or article is electronic, I just copy and paste the highlighted text into my notes.

After putting the text in my notes, I re-read the section and decide if I want to create separate notes for different concepts, people, ideas, and so on. Adding [[ and ]] around the term will create a link to a note. If the note doesn’t exist yet, the link will appear as a dark purple color, but if there is already a note for that link, it will be a brighter purple. In the first paragraph of this example, there is a link for ethnography, but since there isn’t a note for it yet, it shows up as dark purple. Further down, there is a link for virtual worlds and it’s brighter because it links to a note that already exists.

The highlighted sections of the notes are my commentaries on what I just read. Sometimes authors really get going and fill their texts with jargon, so adding my own commentaries helps me simplify and hopefully understand what was read. I think of them as digital marginalia.

At the end of a chapter note, or the Foreword note in this case, I use the Zotero Integration Plugin to add the bibliographic entry for the section of the book. In APA and other styles, it’s possible to cite individual chapters, so I put one at the end. As with the bibliographic entry at the top of the note, I’m not sure if I’ll ever need it, but it’s reassuring to have it ready if it’s ever needed.


It may seem strange to be excited about note-taking, but I am. I wish I had known about Zettelkasten and Maps of Content years ago. With Luhmann’s original card cabinets, his Zettelkasten reminds me a lot of the card catalogs that used to be central to the library experience when I was growing up. More than this, however, the concept of Maps of Content is eye-opening. It’s like creating your own personal Wikipedia. Notes can be long or short, but all that matters is that they make sense to the person who creates them.


Boellstorff, T., Nardi, B., Pearce, C., & Taylor, T. L. (2012). Ethnography and Virtual Worlds: A Handbook of Method. Princeton University Press.

Bonilla-Silva, E. (2020). Color-blind Racism in Pandemic Times. Sociology of Race and Ethnicity, 8(3), 1–12. https://doi.org/10.1177/2332649220941024

Bowler, C. (2021, March 19). Using tags in Obsidian. The Weekly Review. https://chrisbowler.com/tags-in-obsidian/

Miller, T. (2023, January 12). Getting started with Zettelkasten in Obsidian. Obsidian Rocks. https://obsidian.rocks/getting-started-with-zettelkasten-in-obsidian/

Miller, T. (2022, August 30). Quickly Organize Notes in Obsidian. Obsidian Rocks. https://obsidian.rocks/quick-tip-quickly-organize-notes-in-obsidian/

For a few years now, I’ve been using Obsidian to keep a daily journal, and it’s been great. It has a lot of options that I’ve never explored or needed but something came up recently and I wanted to find out how to connect Obsidian to Zotero. An online search using DuckDuckGo returned an unexpected…

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