Obsidian Note-Taking System for Academics & Students - Full Tutorial & Demo (Write Papers Faster)

So 5 years ago, I decided to start a PhD in biology. I was 36 at this time and my

in biology. I was 36 at this time and my knowledge of biology stopped literally somewhere in high school. But that sent me on a journey to research everything I could find about how to learn faster.

I've read the Smart Notes book, the Second Brain book, researched the Zetle Custom Method, tried all the digital tools I could find, and started building

this. That's a digital repository of all

this. That's a digital repository of all my knowledge over the last four years.

Every paper I've read, every claim I've highlighted, every question and idea instantly searchable. So, a little bit

instantly searchable. So, a little bit like Wikipedia, but for my own research.

The big difference to systems like the Zete method or the second brain is that because every claim is verified with references, it can be reused

specifically for academic writing, not just to learn a complex topic. And when

AI came along, I realized that you can also automate parts of this process with really good results. A few months ago, I ended up finishing my PhD 5 months ahead

of schedule and with four first author papers written. In this video, I'll

papers written. In this video, I'll share with you exactly how I built this system, the software you will need, and the strategy you can take to scale it over years. And once we have done this,

over years. And once we have done this, I will show you how to combine it with AI. Now, you might ask yourself, why do

AI. Now, you might ask yourself, why do I actually need some sort of complex information management system? And I'll

ask you this, have you ever played chess? Who wins at chess? It's always

chess? Who wins at chess? It's always

the person with a strategy. So, if you have ever played against someone who has even the tiniest bit of strategic knowledge, they will completely own you and you have zero chances of winning.

And the PhD is exactly like this. You

need a strategy to win. But our

collective solutions are typically very different. Check out this nature study

different. Check out this nature study over here. It says that about 78% of

over here. It says that about 78% of students work more than 40 hours. So in

other words, people grind their way through a PhD. That's like playing chess against a grandmaster and losing over and over and over again. So in the words of Sansu's Art of War, tactics without

strategy is the noise before defeat. And

since a PhD is about knowledge, you need a strategy of organizing knowledge. So

let's build one.

Let's keep it as simple as possible and start with something that everybody is familiar with, the largest repository of human knowledge, which is of course Wikipedia.

Notice something that Wikipedia has nowhere over here any folders. Nothing

tells you where a page belongs to.

Instead, it's organized around concepts that are linked to one another. And if I hover over a single term, then something will pop up and give me the information almost immediately, making it very easy

to access. And additionally, every claim

to access. And additionally, every claim like over here traces back to some sort of paper or some other source that proves why this is true. And then at the

bottom, you will find all of these different books, journals, websites, and so on cited that make up the foundation of this article. But also notice what

you will never find on Wikipedia, and that is a summary of any of these papers here at the bottom. But now ask yourself when you read a paper and try to take

notes on it, how do you go about it? Now

chances are you probably start by summarizing the paper by highlighting and by doing something with the paper.

Wikipedia has none of that. That's

interesting, right? But that's also intentional because that's the only way how we can organize a large body of knowledge. Instead, Wikipedia is

knowledge. Instead, Wikipedia is organized around two main methods. The

first one is links. They connect

different concepts together. What is an evergreen tree? What are the mortaces

evergreen tree? What are the mortaces family? What means endemic and so on.

family? What means endemic and so on.

And the second part are of course the references that separate the speculation from the fact. Let's take the ideas behind Wikipedia's organization but

replace the contents with our own research. So technically each concept on

research. So technically each concept on Wikipedia is a website, right? and you

need a browser like Chrome or Arc to go through these websites and navigate the different links. So for our personal

different links. So for our personal Wikipedia, we're going to use software called Obsidian as our browser and the web pages are going to be text files on

the hard drive. This keeps everything on your computer and allows you to add additional files like the PDFs of the papers you're reading, connect your reference manager, and so so much more.

So here is the plan how we're going to tackle it. First, I want to show you

tackle it. First, I want to show you briefly how Obsidian works. If you know that already, feel free to skip ahead.

There's a lot of good Obsidian content out there already. Second, I will show you how to organize your academic reading in Obsidian so that over time you create something that resembles this

knowledge network of Wikipedia, including all the PDFs and consisting of the reusable blocks that you can then conveniently stitch together to a new piece of writing. And then in the last part, I will combine the technology and

the system and show you how it's all organized. Cuz the biggest challenge in

organized. Cuz the biggest challenge in this entire process is not the technology obsidian and also not the system, how you organize notes. That's

pretty simple. It's this mindset shift from taking sequential notes on papers, highlighting and all that stuff to taking topical notes because without

topical notes, we cannot scale our knowledge repository. [music]

knowledge repository. [music] Let's open obsidian over here. It's now

completely empty because I have absolutely no nodes. If you click this button over here, new note will be created and we can call this node biodiversity and just copy something from Wikipedia so that we have some meat

on this note. Create another note and I'll call it tropical forests and also paste something from Wikipedia. Now we

have two nodes living in our obsidian vault. So this entire vault of knowledge

vault. So this entire vault of knowledge just lives on the hard drive and it has these two notes that I can just open and preview in another application. If

Obsidian started charging you money tomorrow to access your information, you would still have access to it. That's by

the way exactly why I stopped using Notion and Evernote and all that other stuff. The first thing you notice when

stuff. The first thing you notice when you look at Obsidian is that there's absolutely no way to format anything. Of

course, if you double click something and then rightclick and then say format, you can bold and itily can strike through things which makes it a little bit cumbersome. But the main learning

bit cumbersome. But the main learning here is that whenever I bold something or I italicize it, all I get is a small change in the actual text. So in that

case, two stars have been added. And

that is what the markdown format does.

It just adds specific characters to format. But honestly, don't bother

format. But honestly, don't bother learning that format. It's much easier to install a single plugin that will take care of all of that. Just click on

the settings button here. Then go to community plugins and browse community plugins and then find one that is called editing toolbar. It's very very popular.

editing toolbar. It's very very popular.

So a lot of people use it. After

enabling it, you will get this bar here at the top that allows you to do any formatting you want. For example, you could say this is something I want to highlight. So you highlight it. Or for

highlight. So you highlight it. Or for

example, this one I want to strike through or make Italy or make bull. And

all of that is just happening for you in the background. You will still see this

the background. You will still see this markdown formatting happening and changing. But you don't need to

changing. But you don't need to necessarily memorize it all the time or type these characters. And of course, the key thing that you would want to have with your notes is headers. So for

instance, this is a definition. So if I just write definition and then say it's a header two, it will add these two hashtags and create header out of that.

The same way I could add another header risks of biodiversity decline and then highlight this whole thing, make it into an H2 header and then add for example a

note of that. So biodiversity is declining because of climate change.

What I have here is a list. So lists are very easily done by just typing in a minus and a space which will create this bullet point or again you can just use the editing toolbar and for example

change that to a numbered list. So again

you don't really need to learn all of that. There is one feature that I think

that. There is one feature that I think is super super useful especially for academic use and that is called call outs. In the editing toolbar, you would

outs. In the editing toolbar, you would just click this icon over here and then the quotation mark. And then for instance, we could move the definition

into a call out. So I'll just type in three dots so that we can copy content later. So see how it created this nice

later. So see how it created this nice box here and we can just copy that entire thing and paste it instead of the three dots. So now the definition is

three dots. So now the definition is tucked away in this box which looks pretty nice. And a little hack that you

pretty nice. And a little hack that you can do with callouts is you can add a minus here after the square bracket which will make it collapse by default

and then you can just click to uncolapse it. So if I create these callouts I can

it. So if I create these callouts I can choose the call out type and there's quite a big number of callouts. So for

instance if it's a warning I would say alert something is happening then this call out will appear in orange. I know

that some people really love callouts and they even nest them into one another. So, if you are a person who

another. So, if you are a person who really thrives on having different callouts, then install the call out manager plugin because this will help you use callouts much more efficiently

than through the editing toolbar. I

could just briefly show you how I use callouts. For instance, if you go to any

callouts. For instance, if you go to any paper that I have, then typically I have a summary call out and something called author's intentions. So that's for me a

author's intentions. So that's for me a way to tell myself why is this paper written and then what is important to me. That's less of a summary and more of

me. That's less of a summary and more of something to jog my own memory when I read that paper. Another use case would be for example to outsource AI generated

summaries into a call out so that you can clearly see what is AI generated and what isn't. The next thing that you need

what isn't. The next thing that you need to know is how to create links in Obsidian. I'll remove the call out. For

Obsidian. I'll remove the call out. For

instance, tropical forest is something that we already have as a note. So we

can instead of just writing the word create a link to this note over here which is the note on tropical forest and we can link these two concepts together.

So to do this all you need to do is type in the two square brackets like this and then it will bring up a pop-up dialogue which allows you to choose which of the nodes you want to use. So even if I

start writing something like forest, Obsidian will be smart enough to know that name is not starting with forest, but it's just something that's contained in the name. That makes it a lot easier to find the nodes that you want to link

to. And if I click that, it creates a

to. And if I click that, it creates a node to tropical forest. And of course, you can also create links to outside content. For instance, if I have this

content. For instance, if I have this link over here, which is the Wikipedia article where this definition is from, I could copy that and say, um, source Wikipedia,

and then I could highlight the word Wikipedia and just paste the link that I've just copied onto this word. What's

Obsidian will do is create a markdown representation of a link, which is a single pair of square brackets and some round brackets. Now, if I click on that,

round brackets. Now, if I click on that, it will take me to the entry for biodiversity. This is already 80% of

biodiversity. This is already 80% of what you need to know in order to use Obsidian efficiently. But of course,

Obsidian efficiently. But of course, sometimes you need more than text in your notes. You need images just like on

your notes. You need images just like on Wikipedia. So if I just go over here for

Wikipedia. So if I just go over here for instance and take that image and copy that image and I just paste it into my note, Obsidian will edit to the note. So

the very important part here is that this image has been now copied into the vault. That means that everything that

vault. That means that everything that you drop into the vault is copied into it, which will be important once we start embedding our PDFs in this image.

If you click on the button here at the top is essentially also just a link. So

see there are two square brackets and then the name of the PNG file. The only

difference is that there is an exclamation mark in front of it. So if

you remove that exclamation mark, all you have is a link. But if you add this exclamation mark, then this thing is embedded. And that by the way also works

embedded. And that by the way also works for notes. So if I have a note on

for notes. So if I have a note on tropical forest and I put this exclamation mark in front of it, it will embed the entire content of the note into this note. So just remember this

exclamation mark is something that we will need. And by the way, you can also

will need. And by the way, you can also always make this smaller or bigger, however you need to. And that too will be reflected in markdown by this pipe

character and then the number of pixels that goes behind the PNG file. But now

let me show you a slightly more academic workflow and let's try to embed a PDF and create a note on a specific source.

So for that I'm going to first create two folders. One will be our nodes

two folders. One will be our nodes folder where I'm going to put all of our notes that we have created and I'm going to create a sources folder which will be

the folder where all the source notes so all the PDFs and so on will be stored.

And additionally, I tend to do a support folder which contains all the images, embeds, and so on so they're out of the way. Now, let's create a note for a

way. Now, let's create a note for a paper. I'm going to call this paper

paper. I'm going to call this paper 2020.

And then just drag and drop the PDF for this paper. We have a link to the PDF.

this paper. We have a link to the PDF.

The PDF sits here in our vault. We can

put it into the support folder and the Vanvvic 2020 into the sources folder. So

it's nice and organized. I typically

don't tend to embed PDFs in notes because that always messes with the scrolling. If you're scrolling through

scrolling. If you're scrolling through the note, then the scroll is going to get captured when you start scrolling through the PDF. So it's not really useful. Instead, I will remove that

useful. Instead, I will remove that embed. And when I read a paper, then I

embed. And when I read a paper, then I would for instance just open this PDF separately. And you can just pull it

separately. And you can just pull it over here to the side, which creates a split view. So you can have your source

split view. So you can have your source note over here where you can take notes and here on the right side you will start reading the PDF and making annotations and so on. Now let's go to

the very top of the file and type in three minuses 1 2 and three. This will

open the properties dialogue and you can start adding different properties. For

instance, author would be my first property vict enter the journal is PNAS.

So, but instead of typing PNAS, which would be just text, you can add links to the properties. So, if I just type in

the properties. So, if I just type in two square brackets PNAS, this creates a link to a node that doesn't exist yet.

But the moment you click it, this note will appear and will be created here in your folder. The main idea of why we

your folder. The main idea of why we would have notes on journals is that later we can just pull all the papers that are published in this journal and put them into this note which sometimes

can be useful for understanding where you want to publish your own work. Go

back to our Vanvvic 2020. And you can do that by the way with authors as well. So

I could use two square brackets, type in the name of this author, type in enter, and that would add the first author also as a link. I would maybe add one more property, which is the title. And then

we're just going to copy this title over here over time. Of course, you will have many more properties that you can use for your own research like tags or categories or whatever else you're doing that will eventually even replace the

tero. But let me show you why I'm adding

tero. But let me show you why I'm adding these properties by adding another paper and then see how we can pull them together. So I'll create a new node

together. So I'll create a new node urban 2024 and we're going to pull similarly a

paper over here another paper on climate change. Type in the three dashes author

change. Type in the three dashes author arc urban journal science title.

So we have now created basically two nodes on the different sources. They

have some properties and we might want to try to bundle all the papers in our vault. That brings us to one of the most

vault. That brings us to one of the most important and underrated features in obsidian which is bases. A lot of people consider basis quite complicated and too

technical to be part of a standard workflow. I think it's the opposite.

workflow. I think it's the opposite.

Bases are the absolute foundation of using Obsidian in an academic or any sort of structured way. Bases are not that different from an Excel file. So in

an Excel file you have rows and you have columns. Then you can add filters for

columns. Then you can add filters for example to filter your rows by the value of the column. That's exactly what a base does. But instead of rows we will

base does. But instead of rows we will have nodes and instead of columns we have the properties that these nodes have. So let's create a new base by

have. So let's create a new base by using the command plet. Obsidian has

this wonderful feature. If you click command P or control P or just press this button over here, you come to a dialogue that allows you to do anything

Obsidian can do basically. So if I type in bases, then it gives me the ability to create a new base. Let's create a new base and call it papers. By default,

this base just displays all the files in our wallet. That is just how bases work.

our wallet. That is just how bases work.

They take all of the files and then you're going to have to create filters and structure to display the files that you want. For instance, in our case, we

you want. For instance, in our case, we just want to display the files in the sources folder. To see in which folder

sources folder. To see in which folder for something is, we can, for example, go to properties and then click folder.

What we are interested in is basically everything that's in the sources folder.

So if I sort on that then you can really see where things are. To filter you just click filter and then there's a very convenient drag and drop dialogue. So if

I say folder is and Obsidian is already smart enough to suggest the folders that exist for instance sources then this is what is going to be displayed. The

folder property itself at this point we don't really need. So we can take it out but we can add the author the journal the title and so on. So I can even rearrange maybe a little bit. The cool

thing about it is that we can now use this preview feature that Obsidian has.

If you hit command and you hover over something, it will give you the preview of this note. And if you again hover over links in this note, it will give

you the PDF. for example in our case that's why I always add the PDF link somewhere to the top so that I can always drill down to the specific paper

so that's of course not very impressive if you only have two papers let me instead show you how that looks once you progress a little bit here is a base on the papers that are related to a

specific project that I'm working on which is essentially a paper and it creates a base which lists the papers by their rating and there is a summary that

I have written myself about that. So

these are the foundational works and in the same way you can also create papers that you actually want to read. So here

is a list of papers that are a reading list. So that of course features the

list. So that of course features the title and maybe the intent why I want to read this. Here's an example of a larger

read this. Here's an example of a larger vase that contains basically all the papers in my vault sorted or ranked by different years or properties. For

instance, I can have all the papers that released in 2025 and then scroll down and then find all the papers released in 2024. You can create quite elaborate

2024. You can create quite elaborate formulas so that you have all these different icons appearing. So bases are incredibly flexible when it comes to

organizing your knowledge. And as you maybe can already feel like a base like this can easily replace Zotterero for you because Zotterero is just terrible

clunky UI. I don't like Zotterero. And

clunky UI. I don't like Zotterero. And

here I have full flexibility. What is in the rows? What is in the columns? How it

the rows? What is in the columns? How it

is displayed? I can immediately jump into the single paper, immediately jump into the PDF. That's so much faster and more dignified than using Zero in my opinion. Don't shy away from bases. And

opinion. Don't shy away from bases. And

I have links to two blog posts that I made about bases and how you can learn to use them. So armed with this first setup, let's now move on to the second

part where we're going to try to understand how we are going to structure these notes once we have hundreds or thousands of notes because that is where the real challenge lies is to keep a

structure that scales with you and where you can find your notes. That's I think where I made the most mistakes with and I hope that the next part will be really useful for that.

Here's where most people go wrong. To

think note takingaking means summarizing a paper or any sort of source, but summaries aren't that useful. For

papers, you typically have an abstract where someone who knows the paper far better than you spend hours and hours summarizing it. So summarizing is just

summarizing it. So summarizing is just compressing knowledge. So it's easily

compressing knowledge. So it's easily transportable from one person to another. Think of it as a suitcase.

another. Think of it as a suitcase.

Compresses your clothes beautifully. But

try to find any specific item and it gets really really difficult because you have to open the entire thing. You have

to look. You have to rumage through it.

By this time you kind of already forgot what you're looking for and so on. So

what you actually want is a wardrobe.

And that requires a mindset shift in how you organize your clothing or information in that case. So instead of taking notes on sources and PDFs, we

first understand which topics these sources deal with and then we extract the claims a source makes on these topics into the respective nodes. After

experimenting quite a while, I think there are only three types of nodes that you need to ensure that the system works. First, you need source notes

works. First, you need source notes which contain everything someone else is saying. They're not really mutable. So

saying. They're not really mutable. So

you just write them and you forget about them. And then the topic notes which

them. And then the topic notes which contain all the claims you extract from these papers. They are subject to your

these papers. They are subject to your interpretation but not speculation.

Every claim here in the topic note links back to the source note. Number three is the argument or thinking notes which contain your own thoughts, your own

ideas, your own question. So this is a clear separation between what they said, what you understood they said and what you said. So sources, topics and

you said. So sources, topics and arguments is what enables rigorous research in my opinion. And we have already started in our obsidian vaults

to have a source folder and a notes folder. And we have already added this

folder. And we have already added this first paper into our source folder.

Let's try to look at this paper and just try to read what it's happening. so that

we understand how these source notes link back to the topic notes. So for

instance, this passage over here says that evidence of climate change impacts on biodiversity is accumulating. But a

growing literature also reveals highly valuable rates and even directions of these responses. That is something that

these responses. That is something that relates to the concept of biodiversity.

And we have already a note on biodiversity. So let's go to this note

biodiversity. So let's go to this note and basically try to extract that claim from this paper over here into biodiversity.

For instance, we could say rates of biodiversity change are highly variable.

So it is a compression of that claim.

And to make sure that it's not a claim that I'm making but the paper is making, I'm going to add a link to Venvic 2020.

So this ensures that whenever I read something on biodiversity and I think oh that's a really good point that I want to reuse somewhere I know where to double check namely in this Vanvvic 2020

paper. And remember in Obsidian you

paper. And remember in Obsidian you could always hover something with your command key and then it will pop up the contents of the source note which at this time only contains some properties

but is essentially empty and it contains the link to the PDF which helps me open up the PDF. So right now the PDF is of course open here on the right but if you have hundreds of nodes this becomes

really really useful way of actually seeing the raw source immediately in a few steps. And there's a small hack I

few steps. And there's a small hack I would say that I'm using. So if I copy the title of the paper and go to this PDF link and after the PDF I'm going to

type a pipe character and paste that title there. What this does is it will

title there. What this does is it will display the title but actually link to the PDF itself in the background. So

this allows me to hide the PDF behind the title. And if I just add one hashtag

the title. And if I just add one hashtag in front of it, then it gets nicely formatted as the title. And here I could say, okay, well, summary of the paper or

whatever else I want to do like author's intentions is something that I often try to extract, core theory and so on. So whatever else

you would want to add into your source note. Let's do this exercise one more

note. Let's do this exercise one more time. So here for example they say we

time. So here for example they say we propose that this complexity arises because biological processes do not respond to climate in direct and linear

ways. The statement here might lead us

ways. The statement here might lead us to create a new node. So I'll create a new node and call this node biological processes.

I will put it for now manually into the notes folder and just write down that responses

to climate are not linear and again add a link to this Vanvvic paper. But in

addition to that we can go to our existing note and say reason is that biological processes

have nonlinear responses.

So what we did now in addition is that we linked this biodiversity concept to the concept of biological processes where we will have all the other information on that topic of biological

processes and that's already pretty much resembling what you have seen in Wikipedia plus with a little bit more rigor when it comes to sourcing these papers and because we have added this

title and the PDF link it gets much nicer now to look into the PDF. Obsidian

has this wonderful feature where you can link directly into the PDF. So if I just highlight something, for instance, this sentence here says in herbaceous plant

communities, warmer or wetter conditions lead to increased biomass and height. I

can rightclick it and copy this link to selection. And then let's say this

selection. And then let's say this increased biomass and height is a biological process. So it would go into

biological process. So it would go into this note over here. And then I'm going to paste that link. So this link gives me a link to the PDF directly. So if I

hover over that instead of going to the source note, it takes me directly to the sentence in the PDF. That is a really great way of double-checking anything

because for that particular highlight, we say weather or warmer conditions increase biomass and we link to this Vanic 2020 paper. But in reality, it's

not that paper that's making this claim.

It's paper number 24 and 25 in the reference list to this paper. So if I were to site weather, warmer conditions increase biomass and then say it's vanic

2020 that say this, somebody would look it up and say, "Hey, that paper has nothing to do with what you're saying here. It's just a sentence in the

here. It's just a sentence in the introduction." So this is a red flag and

introduction." So this is a red flag and that's why if you have a link to the PDF, you can immediately check whether or not that's true and then go to source

24 and 25 and see who actually has made this claim. Here the convention that I

this claim. Here the convention that I have for myself is the so-called in link. So I'll replace that anchor text

link. So I'll replace that anchor text with in and then I will add the link to the source note itself. So now I have

two links per claim. One of which goes to the PDF only to double check whether the claim is true and one of them goes to the source note itself which allows

it to connect to all the other notes because see what's happening. If I open this Vanwick note and then I go and click those three dots over here and open the back links in the document I

will have all the linked mentions. So

all the other notes that link back to this paper and that tells me to this paper that it deals with one biodiversity, two biological processes and of course as you keep taking notes

over the entire paper you'll have 10 different concepts and you will immediately ground that particular source with the different concepts it deals with. And it goes also the other

deals with. And it goes also the other way around. If I go to biological

way around. If I go to biological processes and you imagine there's like a hundred more of such notes, it will give me a list of papers that deal with this topic. Over time, the topic notes become

topic. Over time, the topic notes become like a mini literature review on that particular narrow topic, while the source notes become gateways to all the

different topics that they deal with. Of

course, it's a little bit cumbersome to always have an in and a ling and have to set it up manually basically every time.

So, this can be automated by using a plug-in called PDF++.

It will also add highlights directly to the PDFs, so you can see where something is linked and what is important and go back and forth between PDF and notes.

It's a little bit of a thing to set up PDF++ and I've added a tutorial blog post so that you can read it up and just set it up for yourself once you are

starting with this system. There's maybe

one addition and when we go to our source node over here, what would you add to this source note, right? It

essentially is just acting as an anchor.

Well, I use source notes primarily to contain the primary source material, which for papers is the PDF itself. But

sometimes you would want to extract specific figures because it really is tightly connected with your source note and not really related to everything else. It just emphasizes the result or

else. It just emphasizes the result or the ideas that this paper presents. So

it belongs into the source note. Hit

command shift 4 on a Mac and highlight that. Then it creates an image and you

that. Then it creates an image and you can just drag and drop that image over here and you have that figure screenshot in here and can start writing your notes and say okay well that's the main idea

of the paper is to present something that's like this cuz this has the benefit that if you are looking at your topic note and you open the source note

you immediately get to see the figure and some interpretation that might be important in the context of this topic note.

But there's of course the case where you don't have a PDF where you're taking notes on let's say a website. Here is an example. It's also a biodiversity

example. It's also a biodiversity article and that's probably something that might contribute to whatever I'm learning or writing. And Obsidian has a

really great way of importing such sources that are not PDFs using an extension called web clipper. So you

create templates and each template imports the source somehow differently.

You select the vault you want to have the folder where you want to import it and then just add it to obsidian. This

imported now the entire page with all the images and with all the text and all the links that it included. So the

source note now is not linking to the PDF but is containing all the information itself. In any way possible,

information itself. In any way possible, you should always aim to have your source note links to either the PDF or the text or whatever the raw material is because that's the only way how you can

doublech check whatever claims you have extracted in your topic notes and trust me you will make mistakes when you extract these claims and over time you're just like what was I thinking cuz

your thinking develops and you get better as a scientist and so you see other things in the same words. Before

we continue, let me just show you how this looks once you have done this for a couple months or years. Here's one of the first topic notes that I have taken

in my vault. And it works exactly how I've shown you. There's one thing that I think is very important to see, and that is that all of these notes are pretty short. So, I call them atomic sentences

short. So, I call them atomic sentences because they're sentences that are basically minimalistic and that you don't need to add anything else to. And

what you can do now is you can treat them as little jigsaw puzzle pieces that you can use to form an entire paragraph of knowledge. You can do it manually by

of knowledge. You can do it manually by just thinking how could I combine all these 25 bullet points into a paragraph or you can ask AI to do that with a little bit of extra prompting. You get a

paragraph that looks pretty much exactly like you would want an academic paragraph to start off. The results will never be perfect, but they will be a really good first draft for a paragraph

on forest, let's say for your introduction section, and it will already contain all of the links to the right references.

The power of these atomic sentences is that over time, they write the papers for you. That's why the system makes

for you. That's why the system makes writing papers so much easier and faster. And double-checking what you're

faster. And double-checking what you're actually writing also becomes easier because you have the notes to the source notes and in the source notes you have the PDFs and in the PDFs you can always

double check all the claims and see all your highlights and so on. There is of course one thing that we have to ask and that is is this type of writing ethical?

Well, I have a story about that and I created a post where I described the system like this and that almost got me expelled from the university. It was a

huge storm to say the least. And

here's a video of how that whole thing went. Watch the video and make up your

went. Watch the video and make up your own opinion. There's one last thing that

own opinion. There's one last thing that we need for our note-taking system. And

these are argument notes. Because so far we have sources made by someone else. We

have topic notes which contain our interpretation of the sources. But where

do we store our actual ideas, our thoughts, opinions, questions, and so on. So that's what argument nodes are

on. So that's what argument nodes are for. You can also call them thinking

for. You can also call them thinking nodes. They are separate from all the

nodes. They are separate from all the other nodes and they contain pure speculation so to speak purely you nobody else. And this separation is

nobody else. And this separation is essential for this academic note-taking system because you need to understand what claims others have made and what your speculation is. Here are a few

examples that I have in my own world.

For instance, this note over here is asking the question, does raising have an effect on range shits? And what I did is I added an email thread that I had with somebody from the scientific

community on that. They had really good points and led me to good papers and so on and so on. Cuz here at the bottom again with the linked mentions, I can see where it was used. And if I wanted

to explore that question further, I would already know where to start because this paper linked to this question. And then over time that

question. And then over time that question note grew by the email exchange with John Campbell. Another way of having an argument note is over here. I

have just written up something. I have

added the sources. I have added bullet point introductions, my thesis aims, the chapter outlines and all the things. So

it's completely me. That's why it is an argument note. The note-taking system in

argument note. The note-taking system in its simplest form consists basically of three types of nodes. The source nodes that are immutable and written by others, the topic notes which are claims

we extract and then interpret and the arguments nodes which contain our own thinking, our questions, our struggles, ideas and so on. Technically, we can have them live in separate folders and

this allows us to use a variety of plugins to style them differently, have different colors and so on. And of

course, there are billion upgrades that you can add to this system. And you

might have noticed already in my vault there, there's a lot of stuff going on that is not standard obsidian. And the

main purpose of that is to make this system more frictionless. Cuz

effectively what I have outlined so far in this video is the concept of how to build a wheel. Yeah. But wheels built a thousand years ago are very different from wheels built today with all the

ball bearings, the rubber coating, the suspension, and so on. So these are improvements that you will over time absolutely discover by yourself if you play around with Obsidian. You can check

out my blog for more tutorials. I've

been writing about it for many years.

You can, of course, subscribe to the newsletter and get a weekly tutorial. Or

if you want a really deep dive, I have an entire course recorded on how to build every single aspect of my vault and contains about 8 hours of video in small chunks and adds you to the

community where you can ask questions.

But that's all just a shortcut because you figure all of these things out on your own. Don't stress about it. Don't

your own. Don't stress about it. Don't

try to learn everything at once. This

will just overwhelm you. Obsidian is

complicated as hell if you start out with it for the first time. To avoid

this overwhelm, let me show you now in part three exactly how I take notes with the simple system that we have built so far without any of this extra coloring

and plugins and so on.

For this demo, I'm going to use the article that we clipped because you don't need any domain knowledge to understand it. Let's first clean up

understand it. Let's first clean up Obsidian. Let's close all the other

Obsidian. Let's close all the other tabs. Close everything in here. But I'll

tabs. Close everything in here. But I'll

just leave a note open here on biodiversity. The way that I usually do

biodiversity. The way that I usually do it is I have my reading on the left and I have my notes on the right and we can for now completely forget about the sidebar. Let's start reading. A small

sidebar. Let's start reading. A small

boy holds enthusiastically in his fishing rod. The lion flies up and the

fishing rod. The lion flies up and the needle spin fish strikes him on the eye.

Desperate to stay outdoors.

So at this point I might already start thinking, okay, maybe that's all just fluff. So we can just skim through it

fluff. So we can just skim through it and see. Oh, okay. Well, the father of

and see. Oh, okay. Well, the father of biodiversity is being introduced here and the man is EO Wilson, the eminent American biologist. I can just reformat

American biologist. I can just reformat it a little bit so that I can highlight that single sentence. In the next sentence, we have in his book, the diversity of life described biodiversity

as an assemblage that has eaten the storms, folded them into genes, created the world that created us. So we could go ahead and say okay well that guy is

somebody who defined biodiversity. So we

could definitely write that down. Maybe

we would say defined by EO Wilson and Eo Wilson because it's a person he might write books. We might

later read that book the diversity of life. So I will create a link out of

life. So I will create a link out of that just by placing the two square brackets. And maybe I would add in his

brackets. And maybe I would add in his book the diversity of life. The

diversity of life itself will be a source note eventually. So I would also make that into a link. So let's first click on the diversity of life and check

that this node is sitting in our sources folder because the diversity of life will eventually be a book. We can

introduce a few properties. For

instance, I could say the type of this is book. I would then add maybe another

is book. I would then add maybe another property which is authors. And you see how Obsidian already suggests the two authors that we have used in this wall.

One is elizabeth bo who is the author of this article and the other one is this van paper that we've been working on. So

now we will add a third author which will be EO Wilson. And as you see, Obsidian already knows of the EO Wilson note even though I haven't created it

yet. So I will just link it and because

yet. So I will just link it and because that is something that I want maybe to read in the future, I could add to myself read it to understand the origins

of the biodiversity subject. And of

course biodiversity itself is a topic that we already have. So I can place it in square brackets to have the link to biodiversity over here.

So the next thing is in his book the diversity of life and we could actually immediately add a link to this book because we already have that note. He

describes the biodiversity and so on and so on. We tend to think of biodiversity

so on. We tend to think of biodiversity as a landscape teeming jungles and coral reefs. It's destruction manifesting as

reefs. It's destruction manifesting as forest clearance and species extinction.

However, these images don't capture the full significance of the equilibrium that Wilson described. Biodiversity is

not just the abundance of life on Earth.

Rather, it is what maintains the resiliency and flexibility of the environment as a whole. That's an

important passage to me as a researcher.

Maybe if I'm studying the concept of biodiversity, all the rest is maybe not so important. So again I'm just going to

so important. So again I'm just going to highlight that part and try to create a note somewhere in my topic note collection here under biodiversity we

could start collecting this idea but even at this point the note for biodiversity becomes kind of a of a dump because there's on the one hand there's a risks of biodiversity decline on the

other hand there's a definition then there's kind of some sort of effects of biodiversity so instead I'm going to create a new node impact effects of

biioiversity decline. And we are just going to copy

decline. And we are just going to copy all of that stuff that we had here previously. Maybe remove that old stuff.

previously. Maybe remove that old stuff.

So I'm going to copy that into this new node.

Add link to biodiversity so that we create this knowledge network. And we

can now finally add this claim. So

decline leads to diminished resilience.

and flexibility.

Notice that I'm adding my interpretation of this because here I'm speaking about biodiversity decline while this source just speaks of biodiversity itself.

That's what I mean by claims that are interpreted by you into the context of your knowledge. From here, we of course

your knowledge. From here, we of course need a backlink to all of this stuff.

add a link to this source. But instead

of just linking to the entire note, which again will be very hard to verify, I want to link to that particular block.

Obsidian has that feature by pressing this carrot key. And here I can select any single block that I want from all the blocks that are in the article. So I

will just add a link to this block. This

adds this cryptic character combination which also appears after the block. But

that makes it easy for me to command hover this and only see the block. And

the highlight itself makes it clear what I'm referring to when I'm linking to this block. So it's the same principle

this block. So it's the same principle as with the PDF, but now twist it slightly differently. And because I

slightly differently. And because I don't want the link to look so ugly, I could just type in the pipe character

and say it's Bokes 2018. So Bes 2018 is the name of the author and Obsidian was smart enough to suggest this to me

because Bes 2018 is stored as an alias for this node and that's another cool feature that you can use to just find things as aliases because aliases help

you linked here a little bit easier.

Let's continue our reading. The global

convention on biological diversity defines its subject as it variability among living organisms at three different levels within species between species and of ecosystems. So we already

have a note on this. I'm just going to open this over here and put it and say defines biodiversity

as we can even copy this part over here.

add a quote and then put it in and say source books 2018 which will link it over here. In recent history, many

over here. In recent history, many species have been reduced to far smaller numbers. Pre-Colus, 25 million bison

numbers. Pre-Colus, 25 million bison roamed in the plains of North America, but by the late 1800s, fewer than 100 remained in the wild. That's definitely

a fact that might be worth saving. So,

let's highlight this and see now we have all these four links here. It would be really nice to be able to switch between them a little bit faster. So, Obsidian

offers the possibility to stack those tabs. If you just click this icon here

tabs. If you just click this icon here and you stack the tabs, then you can just scroll through them horizontally.

Yeah, if you're using a trackpad or an laptop, that's extremely convenient because this allows you now to have one source and like all these different topic notes stacked on the side as you

take this notes because where would this fact go? It could go to general

fact go? It could go to general biodiversity. It could go to impacts of

biodiversity. It could go to impacts of biodiversity decline to but it kind of needs its own node. So maybe examples of biodiversity declines. So let's make a

biodiversity declines. So let's make a new node. examples of biodiversity

new node. examples of biodiversity decline.

And then we could say American bison 25 million goes to 100 in 1880.

And again, we can go to boats 2018 and link to this block with the bison.

If I just type in bison, it will give me all the blocks that contain the word bison and it's only this one. So we'll

just add bison and now we can always double check that particular fact and so on. So I think you get the point that we

on. So I think you get the point that we are slowly building a network of ideas and that we're always reading in the same way. We are highlighting something

same way. We are highlighting something on the left and we're adding those notes on the right. And by the end of this process what you're having is a knowledge network. So if you open the

knowledge network. So if you open the graph view here in obsidian it will show you all the different nodes that we have. Here's our central node of

biodiversity and then all the connected other nodes over here. Now that you have that, you could add a few groups. And

one group could be that the path matches sources, then it wants to be in red. And

another group could be that the path matches notes, then we want this to be in blue.

So that helps us distinguish what is a source and what is a topic node and helps us show this knowledge network over time. That just took us I don't

over time. That just took us I don't know a couple minutes. So let me show you how that looks after 5 years. Here

is my vault again. And if you just open the graph view, there's thousands of nodes. Maybe not thousands but hundreds

nodes. Maybe not thousands but hundreds of nodes for sure. And they're also coded. The green ones are topics and the

coded. The green ones are topics and the blue ones are sources. So very similar.

And we can jump into each individual node. We can see all of the different

node. We can see all of the different connections. So the graph view in itself

connections. So the graph view in itself is just purely visually impressive, but it's not very useful to navigate around.

It just visualize what you have actually created as you went and as you created all these links. Over time, this knowledge network becomes an extension of your mind. Because every time you

take notes, you meditate on the thinking process and you document what you have been thinking as you have been reading all the sources and the connections you have made. And the knowledge network is

have made. And the knowledge network is a reflection of this. And moreover,

jumping into any of these notes allows you to immediately discover tons and tons of different other relevant connections, be it to other topics or be it to sources.

So, I hope this demo makes sense to you and you see how powerful over time that simple note-taking system is and the severe mindset shift that we need, which

is to take notes on topics.

We set out to create a personal Wikipedia for our research that would allow us to write papers faster, find everything that we have ever read, and

also to generate new research ideas. The

key to achieving this was to create so-called topic notes consisting of atomic sentences which naturally over time became narrow literature review

clusters which are super easy to find and which you can update as your knowledge grows on a topic. And because

we took those notes as claims from other papers using these small atomic sentences, we could use them or reuse them to draft our paper much faster. and

even have AI help us in this process.

And the last part where argument notes where we just put our own understanding of the subject matter, our speculation and so on. This trinity of source, topic

and argument is what creates a system that tracks every claim to its source, allows you to express yourself and at the same time grows with you over years

and years and maybe even decades to come. In the beginning, I also said that

come. In the beginning, I also said that generating ideas is a side effect of using that system. So, let me explain this to you. We start here and explore a

note on fossil fuels for example. It

links to another concept which is maybe climate change. Just reading this and

climate change. Just reading this and navigating this climate change note, we might be finding that one of the impacts of climate change on the planet is melting ice sheets. That's another topic

note. And this note is then again maybe

note. And this note is then again maybe linked to your favorite subject, penguins. So a penguin note in itself

penguins. So a penguin note in itself might contain even a reference to a paper that you read just for fun a couple years back about declining penguin populations in Antarctica. What

you did here is actually not trivial because you synthesized a connection between declining penguin populations and the newest fossil fuel emission

reports. You can now consider creating a

reports. You can now consider creating a new idea or question note and ask yourself how are penguin populations impacted by the new fossil fuel emission

projections or something like that.

There are a myriad of tools that can help you find related papers to these two and get you started on the literature review. So the idea itself

literature review. So the idea itself was generated actually by just walking this knowledge graph. We didn't do some sort of idea generation ritual or

brainstorming. It just happened by

brainstorming. It just happened by navigating the network. And that is why the idea generation in this note-taking system is a side product of a well

organized structure. I see it a little

organized structure. I see it a little bit like a garden. Your notes are plants. You saw them. You create the

plants. You saw them. You create the soil for them. You link them. You curate

them in a certain way. But from there, you just have to wait. Yeah. and let

your knowledge network grow over time.

If you did everything right, then the harvesting part, the idea generation, the paper writing, that's actually the fun part. For most people, it's actually

fun part. For most people, it's actually exactly the opposite because they are, so to speak, hunters of information.

Whenever they get hungry and they have to write a paper, then they go hunt for new ideas. They go hunt for how to write

new ideas. They go hunt for how to write all of that. And that takes a lot of effort because you have to find all the papers again, try to upload all of that into your mind and then get to the

writing part. We are farmers of

writing part. We are farmers of knowledge. We planted this knowledge

knowledge. We planted this knowledge maybe years ago into the soil of the knowledge network. And when the time

knowledge network. And when the time came to write a paper, all we needed to do is pluck different notes and create a paper out of it. So the apple was

growing there on the tree. All we had to do is grab and bite it. But keep in mind that once you have eaten your first apple, you are never going back to this pen and paper notes and PDF highlights.

Digital note-taking is literally a one-way street. So guys, this video got

one-way street. So guys, this video got astonishingly long. I'm really glad you

astonishingly long. I'm really glad you stuck around for all of the duration. So

please post your questions and comments below and I'm really glad to answer them or guide you to one of the blog posts that I've written in the last couple years. And if you want to learn more,

years. And if you want to learn more, then please sign up to the effortless academic newsletter. I will send you a

academic newsletter. I will send you a free 21-day course to walk you through setting up this system with all its many components and also add a few more things we didn't have time to talk about

like project management, mind mapping, the different plugins and so on. So,

thank you so much for watching and I hope you make your notes work for you.