Obsidian Vault Tour

Who doesn’t like to have a nosy around someone else’s Obsidian vault?!

Last time, I wrote about three Obsidian plugins that my PhD couldn’t do without. Today, I thought I would like to take you on a tour around my vault so you can see how it all fits together. I want to tell you about:

• The purpose of my vault
• The major structure -> folders
• The minor structure -> sub-folders and tags
• Why this structure works for me

First a caveat; this is absolutely work in progress! I don’t think anyone’s vault is ever finished, is it? Just like our brains constantly evolve so too does our external system to manage that. And for that reason, use this as ideas, as it may not work for you 😀

The Purpose That Obsidian Gives To Me

Before diving into ‘my system’ I thought it pertinent to talk about what I need it to do. Everyone has a different purpose for their personal knowledge management system and we need to bear this in mind when we are creating one for ourselves. That’s why it’s great there’s so many different options out there!

I started with Obsidian back in July 2022 when I realised that my current ‘system’ was about to explode under information overload. I kept forgetting things, didn’t know where to go to find stuff and just generally felt overwhelmed. Just to put it into context, I’m getting close to 1000 peer-reviewed research papers in my vault (yes I’ve only got notes on a fraction of them, but more on that later)!

When I discovered Obsidian, as like many others, I was like WHOA! THIS IS AMAZING! I MUST SHOUT IT FROM THE ROOF TOPS! So I did. Probably told 3 people… and they said;

• ‘ I’m too old for this’
• ‘I’ve heard it’s not very good’
• ‘Yeah I use Google Keep’

I felt hurt. Shocked. But smug. They were missing out. But the reality was their need was(is) different. They have their own paths, own systems and own requirements. Their brains work differently.

I think Obsidian is made for the obsessive to be honest and not everyone is obsessive. And for good reason! Obsidian requires time to curate and grow and tweak. That’s not for everyone. I fell in love with Obsidian for both its simplicity but also its complexity.

So that brings me onto what I needed (and still need) Obsidian to do for me, in the general sense.

What I need it to do, is at an absolute minimum, is that it is able to find anything that goes in there again with some minor searching around. The maximum aim is to have everything so smoothly interlinked, that the time and thinking to do that search is infinitesimal, because I only need to do one rather than 10 searches to bring together any one subject or idea.

I know people talk about the system ‘thinking’ and ‘linking’ for you, but ultimately, it doesn’t. What it actually does is enable you to search a system you’ve curated to your own taste, full of your own ideas about things, and that when you do that search, everything related appears. The better you’ve connected things together when it went in, the lighter the load on your physical brain and the easier it is to put everything together into something new and useful.

I think that with time, systems will become more smart at doing the ‘linking’ and even some ‘thinking’ by having a more intelligent algorithm to work out what it is you are actually talking about, but it will only be as good as the information and notes that you put in. I mean this is starting to happen now, but even if it has an ability to search outside your system, it will use the information that you put in to ‘train’ or ‘guide’ itself.

In essence, put good stuff in and you’ll get good stuff out.

But, I digress, back to the tour.

My Obsidian Vault — The Backbone or Major Structure

I need folders. Some don’t, but I do. I feel like folders are the rooms in a house — you don’t have the toilet in full view of the kitchen, do you? I get the whole open plan thing, but for me that’s a visual catastrophe!

I also like to call things what they are. Much as I like the analogies of digital gardens etc., it takes me too much brain power to work out what is what exactly.

The first thing you’ll notice is that I give folders all capitals. This makes it super easy to tell whether something is a file or a folder! It might seem stupid but the split second difference makes it super quick to allocate things.

It must also be super quick and easy to locate where a file must live. My major folder structure is pretty simple and allocates a file according to the following criteria:

• Is it a Map of Content? (To be honest, I don’t use this folder at the moment. My vault structure isn’t complex enough that I feel I need to. I don’t need a map when I know where it all is… I mean a dashboard might be useful, but I work on such different stuff through the day that it’s not helpful to me.)
• Is it an information source that is written by someone else or provides unbiased information?
• Is it time-based? Like daily notes, journals, weekly reviews, goals etc.
• Is it an idea in progress or a list? Something unfinished and open ended.
• Is is a current project? I.e. my PhD or blog. Something that needs to be finished e.g. a thesis chapter.
• Is it a person?
• Is it a template?

And that’s the major folder structure. Sometimes there can be conflict between 040 IDEAS FORMATION and 050 PROJECTS because it is an idea about a project. But generally an idea is an exploration whereas a project is something with a more tangible requirement. To be honest, in future I may merge these two, but for now, I’m keeping them separate. It’s like keeping the things I want to do separate from the things I need to do.

As a general rule, I don’t use Obsidian as a task manager. I do write to-do lists in there along with goals, but they tend to be more of a brain dump/record rather than maintaining a complex system of to-dos. I find it easier to use a manual system here, along with Outlook calendar, or sometimes TickTick.

To-dos are stressful, and I want my vault to reduce stress!

Let’s move onto the minor structure

My Obsidian Vault — The Sub-Folder Structure

Again, the sub-folders need to be used with minimum effort. Lets break it down a little further. (Hopefully) you can see that its pretty obvious within a folder, where stuff goes.

020 SOURCES

This is the folder I’m spending most time in at the moment as I move all my reading into here. I’ve separated out the information based on the source. Peer-reviewed is everything that comes in via Zotero. If it’s in Zotero, it’s in there and vice versa. These are research papers that have been peer-reviewed and published in the scientific literature. I like to keep these separate from books, which includes Kindle highlights and notes about paper books which are secondary sources. My favourite folder in here though, is ‘My Encyclopedia’. This is a nod to the fact that I spent many hours with my head inside a Hutchinson Encyclopaedia when I was little!

This folder is full of definitions, terms, subjects etc. Basically if I want to know what something is or who has studied it, I head in here. Want to know about general linear modelling or how to calculate how much carbon is in the soil microbial biomass, then head here! I can easily connect my sources to these terms so that if I read a paper where they use a technique, using Dataview, I can super easily bring up that list of papers. It becomes incredible powerful when I can pull together all papers I’ve read that use the technique ‘aggregate stability’, for example, in the encyclopaedia. When I come to put my own experimental results in context, the work is already half done for me!

I also have folders for ‘courses’, ‘talks and presentations’ by speakers and non-peer-reviewed ‘images’ (i.e. ones I haven’t snipped from a research paper). The latter is a catch-all for all images used in the vault.

030 TIME-BASED CONTENT

Everything that is related to a date or time in some way goes in here. This includes all daily notes which I use when I just need to scribble something down, weekly reviews and longer term goals.

(Note 030A Calendar Tasks, the folder for Full Calendar tasks is redundant, I don’t use it anymore; tried it, didn’t like it; I just haven’t deleted it yet.)

Again this is not focused on tasks, just that it relates to a date. I generally don’t find dates a useful way of locating things (because I can’t remember). I do occasionally go through daily notes to reorganise into more appropriate places or ensure that they have a tag so it’s easier to locate later.

I do try to limit my use of daily notes, on the basis I find it harder to find stuff in them. This is because they don’t tend to relate to anything else in my vault (that’s why they are in there and not somewhere else) and can be about really random things, so I rely on tags. At this stage I’m not making a note for each thing that pops into my head in the day. My vault would soon become overwhelmed by notes if I did this, and then thinking about how they connect to other notes, of which there would be too many, so I can find them again would get too complicated. I just want to note something and then I’m done.

040 IDEAS FORMATION

Not the catchiest title in the world, but it does what it says on the tin. This is where ideas go — things that are work in progress or not fully developed. They are optional things to work on. I also include lists, such as gift and ideas lists

050 CURRENT PROJECTS

Current projects go in here. These are things that need to be finished and worked on at the moment.

060 PEOPLE PROFILES

Notes about people… I don’t have many of these, because it feels a bit weird TBH, but they are useful for keeping track of opinions and research areas or Twitter posts for example.

090 TEMPLATES

Just a catch-all for any templates I create. At the moment I only have one for a weekly review.

My Obsidian Vault — Tags

I mainly use tags as a way of connecting raw material and reading status rather than ideas. I find it hard to remember what tags to use, so I don’t want to overuse them or make them complicated. Yes I have a lot in total, but they all fit into 6 categories; #journal, #presentations, #research, #thingsofnote, #writing and #zotero, but within these and since they are context-based, it’s generally pretty obvious which ones I need. I don’t want to rely on tags completely because I quite often forget to use them, or miss one, but they are a great first pass when interrogating your vault with Dataview. I find sub-tags essential to how it all fits together; I can be as coarse or granular as I want.

Why I Have This Structure

I like the combination of tags and folders because its easier to find something than only using one or the other, or neither. That’s what I need; to be able to find related stuff easily. By using a structure based on objective principles, rather than a subjective structure at this stage, finding stuff is more obvious.

Ideas are more subjective and likely to change and evolve, so they need a different organisation structure, separate from the objective one. Think of it like designing the house and the rooms first, then the furniture and interior design are the ideas to come afterwards.

That’s where longform content, canvas, backlinks, dataview and kanban type plugins come in for me. But that’s a post for another day!

If, you want to continue being super curious and want more insight into the research process and personal management with a sprinkling of plant and soil science included, join me in my new free, weekly newsletter, Brain STREAM.