Start using Obsidian for masters thesis, when you already have a rough outline in mind?

Hey, i am about to write my master thesis soon and i am looking for a good tool to manage thoughts and information i gather from literature.

I already have a general idea what the thesis will be about and wrote a proposal, which also contained a very rough outline. So basically it’s time for me to dive into literature deeper now, develop ideas, take notes and finally write the thing down.

My current stack includes:

  • LaTeX + TeXstudio for writing
  • Gitea + Drone CI for version management
  • Zotero for literature management

I use Zotfile to extract notes out of the PDFs, but i am looking for a note taking app, i can expand my thoughts on and write some more stuff etc.

As i was looking for a tool / methodology, i came across alot of people that use Obsidian + Zettelkasten as their knowledge base. I wonder if this could be a suitable combination for me, or if it’s too late to start using Obsidian, when you already have a rough outline in mind.

Do you use Obsidian to build knowledge over the course of months and years to basically have it before - say a thesis - starts, or do some people started using Obsidian to manage notes specifically for a thesis.

The alternative for me would be to just dump my notes into Notion.

Maybe someone else was in a similar situation or can just give me their opinion on this, thanks alot :slight_smile:

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You could definitely use Obsidian + Zettelkasten. The German scholar (sociologist Niklas Luhmann) who has influenced a lot of the discussion around the zettelkasten used it as a professor to develop his writing.

The core idea behind it is that you are going to run into interesting information and chains of thought that are irrelevant to your current thesis. Typically people would discard those ideas / chains of thought, but with the zettelkasten, you create notes out of them regardless because they have the possibility of being relevant to you months or years later.

If you foresee yourself grappling with and interacting with many of the ideas you come across after you finish your thesis, than the zettelkasten would be a good system to implement. Otherwise you could just dump your notes into Notion. Many people use Obsidian anyway for their thesis, regardless of whether they use the zettelkasten method.

For an example, here is a interview I remember on YouTube with a student who used it for her PhD.

P.S. another tool you might want to look into for your stack is Research Rabbit


Yes—I had already finished my dissertation when I discovered Obsidian, but I’ve used it to write or revise conference papers, popular talks/articles, journal article drafts, etc.

My workflow goes roughly like this, but keep in mind that I’ve done most of my writing pre-Obsidian so I haven’t really follow this entirely workflow for a single project. It’s very preliminary but may give you some ideas.

  1. I have to read something. I make a reference note for tha thing using Zotero + the Citations plugin on obsidian.

  2. I read the thing. I take note as I go.

  3. If a note I take on the reading seems important enough that I want to spend more than a sentence or two on it, I create its own note and link it to the reference note. I develop that note, link it to other notes in my vault on similar topics, etc.

  4. If I find I have a cluster of notes around a similar theme, I create an index note on all of them. This could be specific to a work/author (“Human Nature in the Xunzi”), to an era (“Human Nature in Chinese Philosophy”) or more general (“Is human nature good?”).
    4a. Alternatively, if I anticipate gathering a lot of notes about a subject, I might make the index note first, in anticipating of having related notes.

  5. Every time I write a note about a certain topic, I include a link to that topic’s index note. Every time I have a note about a certain author or work, I link to the reference note for that author/work.

  6. Say I want to write a paper about author A on topic N. I look at my index/reference notes for A and N, and check the backlinks section. This shows me all the notes that reference A or N. This gives me an idea of what to write about.

  7. Now I have an idea for a paper, maybe even a thesis for the paper. I create a new project note for this new project, “A’s view of N.” I start adding links to all of the notes I think are relevant to the project, moving them around, writing commentary on how the notes connect, etc.

  8. Eventually, I get an idea for a thesis and how I can structure the paper to prove that thesis. I use headings to create an outline, and then link notes relevant to each section in the outline under that section.

  9. Now I can look at those notes, pull out ideas or passages that are relevant, and start writing the paper.

I know some people do a very hardcore ZK-style of writing where they actually turn their notes into the first draft of a paper. I haven’t done that yet; in fact I find it very useful to rewrite the same idea many times, at different lengths, for different audiences, etc. So my notes aren’t the first draft of the paper. The purpose the notes serve is to organize all my preexisting knowledge and ideas, passages of a book I’m studying, etc., so that I don’t lose any insight I had in the past, and so I might notice patterns and connections I wouldn’t have had it all been in my head.


Thanks so much for the detailed answers.

Some days i ago, i saw this post about Zettelkasten, which made me wonder, if its a suitable approach for me. But i get the idea behind it now, your explaination clarified it for me.

I will definetly check out ResearchRabbit too, i actually haven’t heard about it yet, but it seems to be really promising at finding new related research papers.

And thanks for that explaination of your workflow! I will try to find a similar approach that works well for me. I really hope this will make writin the thesis alot easier.

In the past i used Notion to take notes, and while it looks beautiful it did not really “click” for me. I feel like im too slow and i think about a “beautiful” structure too much, before i even take the notes. I feel like i need to have the idea of the general structure, before putting notes into it. But what if you have no idea for the general structure yet? Definetly hoping Obsidian will work better for me, i’ll definetly try to implement these tips :slight_smile:

Yes, the structureless nature of Obsidian is a double-edged sword, but for me it’s been a plus. I work in the history of philosophy, which means that often a single piece of information can fall under multiple categories. A passage from chapter 19 of the Xunzi on virtue, plus my commentary, might be relevant to (A) a paper on virtue in classical Chinese philosophy, (B) a paper on virtue in contemporary philosophy, (C) a paper on Xunzi chapter 19, etc. With Obsidian, I don’t have to decide where to put it: I can put that single piece of info as its own atomic note (or as a section in a reference note), link it to three different index notes, and then whichever of those three topics I’m exploring, I’ll find the note via the backlinks or graph view.