Zettelkasten workflow for research papers | Zotero & Obsidian link
Summary
TLDRIn this informative video, the host, a computational neuroscience student named Artem, shares his workflow for integrating Zotero and Obsidian to manage research papers effectively. He discusses the importance of a systematic approach to organizing literature, demonstrates how to add papers to Zotero, and explains the use of folders and tags for structuring. Further, he details the process of syncing Zotero with Obsidian using plugins, creating literature notes, and transforming ideas into atomic notes for better retention and application. The video also touches on using flashcards and mind maps for deeper understanding and concludes with a call to engage with the content and subscribe for more.
Takeaways
- π Use a reference manager like Zotero to organize research papers and literature effectively.
- π Zotero helps to store, cite, and collect literature sources, preventing the mess of scattered PDFs.
- πΌ The script introduces three ways to add papers to Zotero: Quick Add, Zotero Connector, and Research Revit integration.
- π Zotero uses subcollections (similar to folders) and tags for organizing items, allowing one paper to be in multiple subcollections.
- π·οΈ The speaker recommends using folders for context-based organization and tags for topic-based organization.
- π The Better BibTeX plugin for Zotero and the Citations plugin for Obsidian are used to sync Zotero's library with Obsidian.
- π Literature notes in Obsidian serve as a link between ideas and their sources, streamlining the referencing process.
- π Literature notes can be used as reading journals, capturing key points, terminology, and personal remarks while reading.
- π The site key is a unique identifier for each article, used to create links to literature notes in Obsidian.
- π§ The script suggests that literature notes can aid in the development of ideas over time, even if they are not immediately turned into atomic notes.
- π The video also touches on using flashcards and mind maps for deeper understanding and memory retention of the paper's content.
Q & A
What is the main purpose of the video?
-The main purpose of the video is to demonstrate how to effectively use Zotero and Obsidian together to manage and process research papers into zettelkasten notes.
What is Zotero and how does it help in managing research papers?
-Zotero is a reference manager software that helps in storing, citing, and collecting literature sources such as books and research papers. It organizes these papers and provides an efficient way to manage and retrieve them.
What are the three main ways to add a paper or a book to Zotero mentioned in the video?
-The three main ways to add a paper or a book to Zotero are: using the quick add feature with DOI or ISBN, using the Zotero connector web extension to clip PDFs from web pages, and setting up a link with Research Revit to automatically add articles to the Zotero database.
How does the video suggest organizing papers in Zotero?
-The video suggests using subcollections (similar to folders) and tags for organizing papers in Zotero. Subcollections can be nested and a paper can be part of multiple subcollections, while tags are used for free-form classification by topics.
What are the two plugins mentioned in the video for integrating Zotero with Obsidian?
-The two plugins mentioned are 'Better BibTeX' for Zotero and 'Citations' for Obsidian, which help in syncing the Zotero library with Obsidian and inserting references into notes.
How does the 'Citations' plugin in Obsidian help in creating literature notes?
-The 'Citations' plugin allows users to search for a target article from the Zotero library and insert a link to a literature note in Obsidian. This note is a markdown file stored in a specified folder and contains metadata from the selected Zotero item.
What are literature notes and how are they used in the Obsidian system?
-Literature notes are markdown files in Obsidian that serve as references to the sources of ideas. They can be used for organizational purposes, as reading journals, or to store atomic idea nodes extracted from the literature.
How can literature notes serve as a reading journal in the zettelkasten system?
-Literature notes can be used as a reading journal by outlining key points, mapping out plans, and jotting down personal remarks and thoughts while reading. This helps in keeping track of the content and ideas from the paper.
What is the role of the 'obsidian to anki' plugin mentioned in the video?
-The 'obsidian to anki' plugin allows users to create flashcards based on certain facts from the paper directly inside Obsidian, which can be used for spaced repetition to commit facts to memory.
How can mind maps be integrated into literature notes to enhance understanding?
-Mind maps, which can be drawn on an iPad and then embedded as images in literature notes, help in quickly refreshing the contents of a paper and understanding how different pieces of the paper fit together.
What advice does the video give regarding the creation of literature notes?
-The video advises not to restrict oneself to a rigid workflow and to trust one's instincts when creating literature notes. If a paper seems irrelevant, it's fine to leave the literature note blank, but if it's relevant, feel free to draw schematics, outline points, or leave it as a reading journal.
Outlines
π Efficient Research with Zotero and Obsidian
Artem, a computational neuroscience student, introduces his workflow for managing research papers using Zotero and Obsidian. He emphasizes the importance of a reference manager like Zotero to avoid losing track of numerous sources. Artem outlines his process of storing, citing, and collecting literature, and how to set up a sync between Zotero and Obsidian. He also discusses his method of transforming research into literature notes and atomic idea nodes, advocating for a systematic approach to reading research papers regularly.
π Syncing Zotero with Obsidian for Seamless Reference
This paragraph delves into the technical setup for integrating Zotero with Obsidian using plugins like Better BibTeX for Zotero and Citations for Obsidian. It explains the process of exporting Zotero's metadata to a JSON file and how Obsidian uses this data to create literature notes. These notes serve as reference points in Obsidian, allowing for easy linking and retrieval of sources. The paragraph also touches on the utility of literature notes for both organizational purposes and as a reading journal, facilitating the extraction and rewriting of ideas in one's own words.
π Enhancing Understanding with Literature Notes and Post-Processing
The final paragraph discusses the value of literature notes for deeper comprehension and memory retention. It suggests using flashcards and mind maps to reinforce learning and understanding of research papers. The speaker shares personal techniques for post-processing papers, such as creating idea nodes and engaging with the material to form a sophisticated and atomic format. The paragraph concludes with a mention of Short Form as a resource for book summaries and insights, and an invitation for viewers to engage with the content and the channel.
Mindmap
Keywords
π‘Zotero
π‘Obsidian
π‘Reference Manager
π‘Literature Notes
π‘Atomic Idea Nodes
π‘DOI
π‘Tags
π‘Subcollections
π‘Citations
π‘Research Revit
π‘Flashcards
Highlights
Developing a zlcast note-taking system involves organizing ideas from various sources like books and research papers.
Using specialized software like Zotero for reference management and Obsidian for literature notes is highly recommended.
Zotero is a free, actively developed reference manager for storing, citing, and collecting literature sources.
Zotero can automatically fill in metadata such as title, authors, year, and journal when adding papers.
The Zotero connector web extension allows for easy clipping of PDFs from web pages.
Research Revit can be linked with Zotero to automatically add relevant research papers to the Zotero database.
Zotero uses sub-collections and tags to organize items, with one paper potentially belonging to multiple sub-collections.
Folders in Zotero are used to categorize papers by context or project, while tags are used for topical organization.
Utilitarian tags in Zotero, such as green for read and fire for interesting, help in visually differentiating papers.
Better BibTeX and Citations plugins are used to sync Zotero with Obsidian for easy reference of literature.
Literature notes in Obsidian serve as a source link and can be used for organizational purposes or as a reading journal.
During the reading process, it's beneficial to outline key points in literature notes to keep track of valuable ideas.
Literature notes can be left blank if the paper is deemed irrelevant or if further development is needed before note-taking.
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Post-processing of papers can involve creating flashcards with the Obsidian to Anki plugin for spaced repetition.
Mind maps can be drawn to understand the paper's content deeply and embedded in literature notes for quick refreshers.
The process of creating literature notes should be flexible and not restricted to a rigid workflow.
The video concludes with an invitation for viewers to share the video, subscribe to the channel, and engage in the comments.
Transcripts
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
you haven't already and press like
button stay tuned for more interesting
stuff coming up goodbye and thanks for
the interesting knowledge
[Music]
you
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