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Organizing Academic Projects with Obsidian Tags and Mind Maps

Academic projects usually span many months or years, and it can be challenging to keep an overview. In this article, I will show you how to leverage nested tags, boards, mind maps, and a few more tools to organize meeting notes, logical arguments, research questions, and more. This workflow is part of what I call Academic Knowledge Management. These methods helped me greatly stay on track during my PhD and, most importantly, not go in circles when asking hard research questions.


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The methods I present here are based on Obsidian, a note-taking tool perfect for academics. If you are not using Obsidian or a similar tool, check out “Why every academic needs to use a note-taking app” and take a look at the Quick Starter Guide to get started.

Organizing Large Amounts of Notes in Obsidian

When it comes to organizing notes, there are essentially only three methods: Folders, Tags, and Maps of Content. In my experience with 1000s of notes I came down to the conclusion that each of these methods is valid for certain purposes. So, let’s look into the pros and cons:

Using Folders in Obsidian

Each note goes into a separate folder, so you can retrieve it later. Obsidian stores each note in a separate file on your hard drive. Folders therefore are just folders on your hard drive as well.

Pro: Intuitive and fast to use. Mirrors the file system.

Con: One note can only be inside a single folder. This often leads to conflicts. At scale folders are just as hard to find as notes.

If you want your folders to appear colored like in my screenshots you need to:

  1. Install the “Style Settings” plugin
  2. Use a theme that supports this setting. I am using “Chime Theme”.
  3. Go to Settings > Style Settings > Chime Theme > Folders to enable the color.

I suggest using folders only for the broadest categories and never for retrieving information. If you are unsure which folder to put a note in, you should make the folders broader so they become unambiguous again. This makes it easier to work with folders in the long run. At scale, folders break down, and you look for the folder just as long as you look for the note.

Using Obsidian Tags to organize notes

Each note gets one or more tags, e.g., #meetingnote, to identify its purpose. Since tags bind multiple notes together, they can be seen as folders. I highly recommend the TagFolder plugin if you are working with tags, as it allows you to view your tags as folders.

If we think of tags as folders, nested tags are subfolders. Write #paper/ecology/review, for example, to create a note that is an ecology review paper. We will see the advantages of this further below.

Pro: Allows for very flexible structures. One note can have multiple tags (not possible with folders).

Con: Leads to organization fatigue and duplicate tags. Often feels like too much effort.

TagFolder is a plugin that displays your tags as an actual folder, like in the screenshot above. It lives in the left sidebar. Unfortunately, the native implementation of tags in Obsidian is not very well done, but this plugin fixes it for us. Note that it also works with the rainbow folders (described above). For renaming and restructuring tags, use the TagWrangler plugin. Both are popular and well-supported plugins.

Organizing your Notes with Maps of Content

Maps of content are notes that simply link to other notes, and you can enrich them with annotations. There are no special rules on how to structure them other than that they should optimize the overview you get from looking at the note.

Pro: Notes are stored in a context and their relationship is hinted at. Best possible overview.

Con: A lot of manual work since you need to update them manually every time a related note is added.

In this example, I organize different traits that ecologists measure on plants by the underlying biological function, e.g., growth rate or photosynthesis. The trait SLA (Specific Leaf Area) is used in multiple lists. This is the flexibility you can have with maps of content. Use a separate map of content for each purpose you have. Here, the purpose is quickly finding which functional traits are proxies for which biological functions. But I might also sort the traits by the papers that discuss them and create a separate map of content for this.

What is better Nested Tags or Regular Tags?

Nested tags create a hierarchy of tags and extend the functionality of simple tags, making it easier for you to remember and reuse tags. I use two to three layers to identify notes in big projects. This is a good trade-off between complexity and organizational power. The three levels are:

  • Project: The project this note belongs to (see next section). Usually, I use a short tag to pull together all notes related to a project. These can be papers, meeting notes, research questions, etc. Using only the project tag would leave me, however, still with 100s of notes to sort through whenever I am looking for something specific.
  • Type: The type describes what type of note this is. Examples are papers, meeting notes or progress notes.
  • Descriptor: This layer is optional but sometimes feels necessary. For example I subdivide my meetings notes by the person I had the meeting with like in the example below:

Nested tags allow you to create these hierarchies, and Obsidian supports displaying these tags hierarchically right out of the box (Click the button in step 4 in the screenshot in your tags sidebar). The key here is to keep the project identifier short so that you can remember it easily. This way, Obsidian will suggest the valid tags in a small popup, and it will be easier to tag your notes.

Note that a note tagged #Project/Type/Description will be found when searching for the tag #Project or the tag #Project/Type. This will not work if you use the tag `#Project-Type-Description` (all in one word) because this would create a new and unrelated tag for each unique project, type, or descriptor value. Nested tags, therefore, are a great way to group your notes hierarchically.

The Project Note: Central hub for your organization

In the previous section, we used “Project” as the first part of a nested tag. A project is a map of content for all notes that relate to a project. In my case, I aim to map a project roughly onto a paper I want to publish or an idea I am writing about. They can be pretty extensive and bundle 100s of related notes. Let’s look at an example:

Each project gets a concise tag that will be used to identify all notes related to this project. From here, the contents adapt to the subject matter. My typical contents of a project note are:

  • A table of research questions that I am exploring in this project. Each of them has a note with more details.
  • A list of ideas. These are precursors to research questions as I do not put much thought into writing them down, and they might be redundant, trivial, or irrelevant. Ideas are just a scratch pad to keep creativity going. Creativity grows with every idea you generate, so it is worth building this skill.
  • A list of papers that are related to this project. Especially key reviews on the subject or papers introducing methods you want to employ. It is an excellent way to prepare for your literature review. Later, you can even use AI to extract the most important of these papers for your introduction.
  • Links to data sources or technical documents. Surprisingly, often, I end up reading through manuals for protocols or computer infrastructure. You can use your project note as a bookmark manager.
  • List of meeting notes. If you are talking to collaborators, it is sometimes worth copying and pasting emails into your notes or creating summaries about meetings you had. This way, you never forget key decisions during a project’s lifetime.
  • Extend this list with your own ideas…

A project note can benefit from a few plugins automatically pulling the notes together. Check out this long thread with many more details. For example, we can retrieve all meeting notes with the tag vcp/meeting. This query will extract the descriptor (word after the second / in the tag) and display it. Every time a new note is added, the table automatically updates.

This is a fairly complicated use-case but it is worth it for large projects. Here are the basics of creating dataview queries.

Structure Arguments using the Canvas

While the project note structure helps you bundle all your notes together, it is usually not the best way to store information and insights. For this, we can use two tools:

  • The Obsidian Canvas, a built in mind mapping tool for more quick and dirty sketches
  • Draw.io for more professional and well annotated flow of ideas.

Both of these methods help us structure logical arguments so that we can spot problems with our arguments.

Using Obsidian Canvas to Store Insights and Build Arguments

The canvas is Obsidian’s name for a mind map. Your elements can be either notes from your vault or snippets of text called cards that live only within the canvas. Then, you connect these and annotate the connections. It is a compelling method. In this example, I do three things:

  1. I store notes on key papers
  2. I extract key figures from each paper and lay it out next to the note on the paper.
  3. I connect these notes to questions and to one another.

The key to a successful mind map is a reasonably well-defined “visual language” you agree on. Make it as simple as possible. The legend I used in the video above is blue for questions and red for problems/weaknesses. That’s it.

Don’t get stuck on a language that has to be perfect. In my opinion, the canvas is all about quick and dirty. It is ephemeral, and you can use it as a scratch pad to jot down progress. Here is a much more elaborate example where I keep track of progress cracking a complex data problem.

On the left are questions that I later color green or just add a ✅ emoji to symbolize that this question has been answered. The plots provide arguments answering the question, and then there are more questions on the right. So, any box that is not green is a potentially open question. Perfect for keeping track of every rabbit hole.

Using Draw.io to store insights

Draw.io allows you to create mind maps with more depth. You can use different shapes and more colors and specify how the connections run. Here is a more complex example of storing insights generated from reading dozens of papers.

Again, it is all about visual language. Try to define for yourself what things mean, and you will slowly notice how this one mind map stores months of learning and understanding. Here is what four months’ worth of reading looked like when I studied molecular biology:

The blue pills are proteins. Arrows indicate different types of interactions. Green boxes indicate processes. Together, this displays how a cell reacts to stress (or a small subset thereof).

Use boards to keep track of open tasks

Boards are a great way to organize daily and quickly changing tasks. I recently created a video explaining how I plan out every week ahead of time. Here is how it looks.

Boards can be used to prioritize your papers, organize your writing process and many other small tasks. The idea is always the same: Create something you want to get done, weight it by priority and then move it from the left to the right on the board. Learn more about organizing your literature review in this article.

Summary

In this post I presented five methods I use to organize big projects:

  1. Structure your notes using nested tags and the pattern project/type/descriptor.
  2. Create a project note to bundle all notes related to a project.
  3. Use Obsidian’s canvas to track progress and build arguments.
  4. Use draw.io to efficiently store everything you know on a topic visually.
  5. Use boards to organize daily/short todos.

If you want to dive deeper into organizing academic projects with Obsidian, check out this course:

This course will teach you the exact workflows I’ve refined over years to organize a growing, massive collection of 330.000+ words in notes. If you want to transform your research career, this course will be a leap forward.