Select text to annotate, Click play in YouTube to begin
00:00:00
when you develop a zlcast note-taking system everything comes down to ideas the majority of them come from sources like books and research papers and not to get lost in this sea of references i
00:00:11
highly recommend using a specialized software a reference manager like zotero and a system of literature notes inside of obsidian today i will show you how i effectively use zotero together with obsidian to turn research papers into
00:00:25
xenocast and notes if you're ready buckle up my name is artem i'm a computational neuroscience student and researcher here we talk about the brain both the theory of how it works under the hood as well
00:00:43
as practice of how to study and learn more effectively if you're interested consider subscribing to the channel not to miss anything the video is structured in the following way first i will talk about what zotero
00:00:54
is and how i use it to store and organize my research papers next we'll see how to set up the sync between your zotero library and obsidian and finally i will show you my workflow for
00:01:06
processing the information from reading the paper to what's called literature notes to zerocasting atomic idea nodes so let's go you probably know that zotero is a reference manager a piece of software
00:01:20
that allows you to effectively store cite and collect literature sources mostly books and research papers remember how you downloaded your first research paper to read and lovingly put
00:01:32
it on a desktop or in the folder somewhere well when you have 5 or 10 articles it works just fine but once you get into that start to look for information everywhere things soon get pretty messy
00:01:46
pdfs lie everywhere on desktop in folders in the cloud and it's almost impossible to find anything you forget what you have already read what you've only started reading and what you have
00:01:57
saved for later that's why i think it's vitally important to start a systematized approach as soon as possible even or especially if only are just starting to read research papers
00:02:09
regularly i recommend using some sort of a reference manager personally i went with zotero mostly because it's free and under active development basically zotero is like a first hub where i put everything i might want to read at some
00:02:23
point now there are three ways to add a paper or a book to zotero the first one which i use most common is the quick add you just click on the magic wand paste the doi or esbn and boom the paper is in
00:02:37
your collection all the fields such as title authors year journal are filled in automatically sometimes if the pdf is available online zotero will attach it there is also a
00:02:49
zotero connector web extension which allows you to clip the pdf from the web page and finally an absolutely amazing new feature is if you use research revit to discover
00:03:00
relevant research papers by the way i have a video about it right here you can set up this link with your zotero account so now every article you add on research revit will automatically appear in your
00:03:13
zotero database how cool is that now after you add a paper to zotero using any of the options it's time to find every article its place the tarot uses two main ways to structure your items the first one is called sub collections
00:03:26
it's very similar to folders you can nest them in one another but the key difference is that one paper can be a part of multiple subcollections if you don't mind for convenience i will say folders from now on meaning the sub
00:03:39
collections and the second one is the tags system and classification with folders versus tags is like vain vs emacs it's an everlasting debate but here's the approach that i found to be most useful i use folders to break up
00:03:53
papers in their contexts where i will expect to apply the corresponding knowledge you can think of that as projects in a new sense i have a separate subcollection for lab research projects where i dump all the relevant
00:04:06
papers when i prepare a presentation for example i create a sub collection for that and collect my sources there similarly i have nested subcollections for youtube videos tanks on the other
00:04:17
hand serve for organization by topic when i add a new paper i usually populate it with tags in a very free form anything that comes to mind for example i'd say that judging from the abstract this paper is about hippocampus
00:04:31
place cells remapping and i'll take it with optogenetics as well since that was the primary method then i can filter the entire library or any subcollection by tags to discover papers on a particular
00:04:43
topic there is also a couple of utilitarian tags with color to visually differentiate between the papers for example i have a green emoji tag to symbolize that i've already read this
00:04:55
paper fire means that it's really interesting and i should read it as soon as possible or continue reading it if i already started so let's see how to easily reference all of this treasure inside of obsidian to do this we are
00:05:08
going to use two plugins one for zotero called better bibtex and one for obsidian called citations not to make this video too long i won't go through the installation process but in
00:05:20
the description you can find links to the plugin pages which contain really easy to follow installation instructions so once you have better bibtex installed select my library and click export there
00:05:34
select the format to better json click keep updated and select a place where you want to save it the logic behind this process is like this this file is basically a json document
00:05:47
containing metadata for all of the items in your zotero database things like titles authors years source urls etc and the banner bibtex extension overrides this file every time you add
00:06:00
items to your library so at every point in time this file updates to contain most recent state of yosetera then we will tell obsidian to take this
00:06:13
file and pull out references from there so let's do that in obsidian install the plugin called citations and don't forget to enable it now go to settings plugin options
00:06:25
citations copy the path to the json file we have just exported from zotero and paste it to the citation database path field if everything is okay obsidian will tell you
00:06:38
that it has loaded successfully and don't forget to configure the folder where obsidian will put all the literature notes we will see what they are in just a second so suppose when you write down the idea you
00:06:51
want to mention the source it came from i always recommend doing that because at some point later down the road you might want to research more about the topic if it came from a paper which is a part of
00:07:03
your zotero database then lo and behold you don't have to go to zotero and manually copy and paste the diy of the paper into obsidian which is cumbersome and looks of ugly just press ctrl shift
00:07:17
e if you are on a mac or go to the commands page and search for citations insert literature note this will bring up a field where you can search for the target article and press enter you can
00:07:29
see that we automatically inserted a link to a funny-looking note starting with the add symbol this string is called the site key a unique identifier for each article these notes are what i
00:07:42
like to call literature or reference notes if you click on it you'll see that it's just a usual markdown file stored in the folder for literature notes we specified earlier essentially
00:07:54
what the plugin does is that it pulls the metadata from the tarot item you select and inserts it into the freshly created note if you reference the same article somewhere else it would just
00:08:07
insert a link to this existing literature note and not create a new one but what is the use of such literature notes well for starters and this happens most often these literature notes can
00:08:19
just remain empty and serve purely organizational purposes that is when i create an idea node in this little casting folder and i want to link it to the corresponding source i don't have to
00:08:31
go to zotero every time and manually copy and paste the title and authors stuff like that instead just easily insert a link to the source in a couple of clicks moreover you can navigate to the
00:08:43
literature node and use the local graph view to see what valuable ideas this article served as a source of like some sort of a visual atomic summary of the paper two
00:08:57
they can serve as a reading journal when you read with the zero casting system in mind you're always looking for opportunities to extract valuable ideas from this text rewrite them in your own
00:09:09
words search for interconnections and store them for later but quite often this transition is just impossible to do on the go as you read what you would consider as a single atomic idea note
00:09:21
could be actually spread out over a handful of pages and as the author takes detours provides examples and elaborations you might run out of memory stack so to speak that's why i like to
00:09:33
outline key points as i'm reading mostly to keep track of what's going on i use this space in these markdown literature notes to keep a sort of a reading journal where i map out the plan key
00:09:46
terminology author uses jolt down my own remarks and thoughts a note of caution though don't feel obligated to transfer these literature notes into atomic zeddles right on the spot
00:09:58
it may turn out that certain ideas take several chapters to fully develop before they are ready to be promoted into the zenocastin folder sometimes even after you finish processing the source it's not enough to
00:10:12
fully connect the dots and crystallize certain ideas and it's totally normal only months later when you encounter something similar somewhere you realize wait i've already seen it there you go to the
00:10:24
reference note and everything is laid out in front of you you go through that information again and together with fresh formulations and details you've just met in the different source it reaches the critical mass to be
00:10:37
rewritten in a sophisticated simple and atomic format one potential source for such new perspective is the today's sponsor short form this is an amazing platform which provides what i would call book
00:10:50
summaries on steroids they are far more comprehensive than the ones you'll find in blinkist and contain interactive exercises and author insights there is already quite a variety of genres being
00:11:01
covered such as science education and psychology and i've been pleasantly surprised with how often they publish new book guides i personally use short form to filter out the books that i want and don't want
00:11:15
to read as well as using their brilliant summaries to enhance and refine my literature notes before transferring ideas into zeddles to get 5 days of unlimited access and 20 discount on
00:11:27
annual subscription join short form through my special link or click the link down in the description after i'm done reading the paper which hopefully led to adding some idea notes into the zl custom folder sometimes i do what i
00:11:40
like to call post processing of this paper this relates to a variety of things you can do to commit certain facts to memory and to get an even deeper understanding of how different pieces of the paper fit together one
00:11:53
thing you can do is make use of space repetition now this is a topic for a separate video which they will probably do in the near future but basically you can create flashcards based on certain facts from the paper
00:12:05
and the plugin called obsidian to anki allows you to write your flashcards right inside of obsidian i use these language notes as containers where i store the questions and answers for the flashcards another option to get a
00:12:18
deeper understanding is to draw a mind map of the contents of this particular paper i usually draw my mind maps on the ipad and then simply embed them inside of literature notes as images that way
00:12:31
when i visit the reference node file i can refresh the contents of this paper in my memory within seconds and see what it was all about of course this is quite time consuming so i don't do it very often only when deep down i know it's a
00:12:44
great idea for example if the paper is directly relevant to my research and the same is true for all of the topics i've mentioned before there is nothing you pronounce must do every time you create a literature note the way i personally
00:12:58
write them is completely free form i'd say just trust your god and go with the flow if you feel like you want to draw schematics and outline a few points doing if on the other hand you feel like the paper is wishy-washy and not really
00:13:10
irrelevant then don't stress too much about it and leave the literature note blank this is completely fine as well don't restrict yourself in some rigid workflow because this is a creative process not a
00:13:24
production pipeline that's all i have for today if you have any specific questions or topics you want me to mention don't hesitate to leave a comment down below if you liked the video share it with your friends subscribe to the channel if
00:13:36
you haven't already and press like button stay tuned for more interesting stuff coming up goodbye and thanks for the interesting knowledge [Music]
00:13:57
you
End of transcript