A PhD student facing difficulties with his 6 months ZK

Knowledge management
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I started a sort of Zettelkasten a few months ago, at the beginning of my PhD.
Now I’m facing several difficulties in my real life practice, so I take a break to think about my overall reading and note taking process (which is my main activity for now).
I do believe in the ZK method, but I need my ZK approach to meet my needs as a PhD student.

  1. Efficiency : I read too slowly. I want to capture each concept I read about, considering that it may be useful, either for my personal understanding of wider concepts, or in a more practical way (choose an experimental technique for example). Maybe this is not a methodology issue but only self management…

  2. Atomic vs. consistency : I spend a lot of time thinking before noting “simple” things : where should I note this idea/information ? Should it be added to an existing note ?
    Lets take an example : I often deal with physical phenomena. What should I do with phenomena that are closely related, either because of strong interactions or because they are part of another phenomenon, or not fully meaningful on their own ? I end up with many “index notes” describing physical concepts, with links to smaller notes that I try to make “atomic”, but this process sometimes seems artificial to me…

  3. Organisation (related to point 2.) : I have an INDEX note with some entry points to my ZK, for example “Friction” which is a major field in my work. The “Friction” note is an index note in itself, containing a mix of explanations (as short as possible), divided in chapters, and links to smaller notes. I am more and more uncomfortable with this approach, but I feel stuck.

  4. Maintenance : I have set up a tagging system to manage the notes status (from fleeting to permanent, loosely based on evergreen notes). Besides, I have a few folders : “Inbox” (fleeting), “Notes” (for what I consider permanent notes), “Ressources”, “Projects” and a few others.
    But I don’t invest much time in the “maturation” process : basically, as soon as a note has links to others, I move it to “Notes” folder, with the lowest “maturity tag”. I know that some of this notes are still very incomplete and naive. Am I right to bet on a future visit the next time I address this concept to improve the note, or should I schedule the “maturation” process ?

I would really like to have a more “natural” note-taking process, which would still be ZK-compliant…

Thank you for reading my post to the end, and for any guidance you may give to me!

PS : also posted on Research & Reading — Zettelkasten Forum

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Hi TriboKiv ! I’m also in research and it took me time to fine at structure that corresponds me, although I still upgrade/refine my Obsidian structure. I put though on how I deal with your issues. It doesn’t mean it’s better but it matches my way of working, taking notes and learning

For efficiency: if new concept arise from an article, I have a note only for this article and write thing on it, using Zotero too. When it’s very small concepts that you don’t know where to put, you could just have an “on-the-fly” note on which you just put random new things at the moment and that you can pick up and refine later on.

Atomic vs. consistency : In my case I’m using MOC (map of content) that are just an index/aggregation of other note or ideas. This is kind of a parent note connecting to others. But I’m also having similar issues. Should I put “climate change” and “extreme events” in the same note? Just keep in mind note are not a static thing and can be split or merge depending on the content. However, most of my notes are going in a PERMANENT folder that gather information on many independent topics, avoiding to have to select a folder to put them to.

Organisation: that’s what I mentioned as MOC. Most of the time I don’t right paragraphs but more ideas, links to other note. When it’s a big topic that relates to dozens of note I make small sections. But not sure I’m really helping you.

Maintenance: don’t put too much pressure on yourself. It’s just where you decide to put the cursor. I personally don’t care to have a note with only one paragraph. I like my PKM even if it’s not perfect. I think it’s just a long term process to build you’re own personal wiki and that’s exciting to me.

Cheers!

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And here is the structure I use with the 2 biggest folders being “20_LITERATURE” (scientific articles linked to Zotero) and “30_PERMANENT”

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Wanted to reply, not because I have a solution, but because I’m experiencing a similar problem (going into the later stages of my PhD!).

I am currently in the midst of a dash to read as much background as I can in a related area, and find that I am getting slowed down significantly, despite my best efforts.

My workflow is roughly - create a note in Obsidian using the Citations plugin, then try and write minimal (unlinked) notes as I go for your standard “Objectives”, “Methodology” etc headings. If I see an interesting reference, I’ll note that down the bottom with a quick reason why it’s interesting. If I have a thought or related idea, I try and add that under a ‘my thoughts’ section. These are both to prevent me from getting out of the reading flow too much: either going reference hunting, or creating new concept notes and then being distracted by thinking of all the other literature or concepts I could connect to this new concept.

It’s not really working though. I keep seeing ideas in new literature and thinking “hang on - didn’t I read something in a past paper about this?”. Either I did record it, and it becomes a voyage through (back)links to find it, or I didn’t, and now it’s a CTRL-F journey through pdfs. The latter problem is obviously something I could defer, but it motivates me to write even more thorough (and time consuming) notes just in case an idea becomes useful in argument or as contrast. This is not feasible with the reading volume I have, but I find it difficult to find the “good enough” level prospectively.

The other pain point is trying to clear up the noise of linked notes. Sometimes I link to a concept because the current article supports/evidences/refutes it, and sometimes because it is just related. Furthermore, because I don’t want to get sidetracked while reading, I write the context for why the article evidences the concept in the literature note. Together, this means that the concept note itself is often blank, and the back links are full with a variety of different types of links to dig through.

I think part of the problem is I have quite specific ideas in the concepts (e.g. “Many systematic reviews do not adequately search grey literature”), which leads to having lots of small and closely related notes. Some may be duplicates, but others are subtly distinct, and it adds to the burden of post-processing a literature note to ensure it is sufficiently linked to all the related concepts.

I somewhat align with @arthurocrome (single note for the article, one flat folder for all my concept/idea notes, and some quasi-MOC distributed throughout - though these are hard to keep up to date, and most aren’t).

I would agree with your thoughts in point 2 - you risk creating your own formal ontology if you try and categorise things too strongly, which imo creates rigidity and friction in note taking, particularly as your knowledge evolves. As for maturation, in my experience this happens naturally as you revisit notes. Having an ‘evergreen’ label is too much pressure for me, particularly as things that once seemed atomic fragment over time (e.g. one note “The performance of automated screeners…” became many → “The performance of (semi-)automated…”, “The performance of active learners…”, “The performance of LLMs in…” such that the original was no longer relevant).

Obviously - take my advice with a pinch of salt, it’s a bit frantic here. With a deadline soon approaching I hope the work pays off, but I can’t help but feel like I’ve invented more work than it’s worth. (I should note I don’t adhere to ZK, but the problems seem similar)

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I was also confused at the beginning. I wanted to write down everything I read for I thought they might be useful someday in the future. And I felt like that taking notes of concepts was like copying the book at that time. Writing down everything is obviously impossible. Now I manage my ZK notes in an easier method. I may not be right, but since it works for me, maybe it’s worth sharing.

ZK is better for note-taking with specific interests——a problem that needs an answer, a niche topic that worth exploring, or a debate that requires some research. A clear direction will lead readers to resources that can build relationships. Then propositions and arguments related to this specific topic can be put together and linked in a way that make sense to the reader.

The thing is, with ZK system, only what’s related to the interested topic will be written down. The note taker must know why the resources in hand worth reading. Why it is important? Why do I want to take notes of that? How will this note contrubute to my goal? For example, what do I want to study about Friction? Maybe the application in real world? Or just the pure theory? The authur of the book How to Take Smart Notes said something like this in an interview: you must know where a note belongs to when you write it down. I don’t remember his exact words, but I interprete it this way.

The truth is that the ZK note-taking shall be slow because readers must take time to think and spot valuable sentences. A clear objective can make it faster. A streamlined process also do. If frequent tagging is painful, will a templete make it easier? This is my example, I am reading about video game history now. I can simply list year and event and then finish the reading, but that wouldn’t make any sense to me. Then while reading about historical events, I keep asking a lot of questions. Why this happend? Why successful? Why people 30 years ago like this? Who invested in this project and why? These questions can lead me to different areas, some to marketing research, some to player behavior study, some to culture or media study. Then I pick a new goal to continue. These fields of study sounds big, but actually I only focus on one event or a sequence of them. Usually I stopped exploring once I got the answer I wanted. Curiosity knows what’s important and what to ignore. But I’m not a PhD… :joy: I have a background in marketing, so most of the time I study the industry and consumer. I know it’s different.

I create permanent notes at the same time I take literature notes as long as I know where they should go in my knowledge system. Otherwise I would ask myself if it’s necessary to take a note of that. It saves time for me because I don’t have to maintain them afterwords. I also use index to organize them. I think indexes are fine.

Hope this is helpful. I took about 2 months to build the whole system, testing about linking, tagging, organizing and so on, trying to find a solution that make me feel comfortable and willing to take notes. When a solution was chosen, the note-taking process can go smoother. Only slight changes were made.

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Thank you all for your inspiring answers.

I took some time to think about it and experiment… What I’ve learned so far is that it is a never-ending process!

During the first months I read articles and book chapters with the aim of “getting into the topic(s)”, and some of theses readings were “just in case”. After this stage I understand more clearly what @ThoridalFury recalls by quoting “How to take smart notes” : you must know where a note belongs to when you write it down, so you should read with a goal in mind. If the reading doesn’t serve any known or anticipated purpose, don’t spend time writing notes.

I appreciate your other comments which have already helped me, or will be worth rereading later.
For the moment, I have not yet begun any consistent writing process, but it’s important to anticipate how the PKM should help during this stage.

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@ThoridalFury Even if there are always small changes, it took me also around 2months to figure out the main structure of my vault. It’s easier to work in it afterwards.

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I don’t know if you use Zotero to manage pdf files, articles, etc but for my research Zotero Integration plugin is game changer. The possibility to load directly your notes, highlights, etc make everything smoother.
I cannot recommend more those Template/workflows that I adapted for my need:

It takes a bit of time to implement but it was worth doing it to me.

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You’re absolutely right!
I already use it so that my Osidian notes can refer to my “literature notes” written in Zotero.
I managed to have 2 ways sync of my Zotero notes but in the end I don’t really need to edit my zotero notes in Obsidian.
The game changer for me is to link my ZK notes to a specific part of a Zotero note, and being able to open the source pdf in Zotero within a few clicks.