Zettelkasten workflow for research papers | Zotero & Obsidian link

Summary

In 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

• 📚 Use a reference manager like Zotero to organize research papers and literature effectively.
• 🔍 Zotero helps to store, cite, and collect literature sources, preventing the mess of scattered PDFs.
• 💼 The script introduces three ways to add papers to Zotero: Quick Add, Zotero Connector, and Research Revit integration.
• 📁 Zotero uses subcollections (similar to folders) and tags for organizing items, allowing one paper to be in multiple subcollections.
• 🏷️ The speaker recommends using folders for context-based organization and tags for topic-based organization.
• 🔗 The Better BibTeX plugin for Zotero and the Citations plugin for Obsidian are used to sync Zotero's library with Obsidian.
• 📝 Literature notes in Obsidian serve as a link between ideas and their sources, streamlining the referencing process.
• 📘 Literature notes can be used as reading journals, capturing key points, terminology, and personal remarks while reading.
• 🔑 The site key is a unique identifier for each article, used to create links to literature notes in Obsidian.
• 🧠 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.
• 🎓 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

00:00

📚 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.

05:02

🔗 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.

10:04

🌟 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.

Keywords

💡Zotero

Zotero is a reference management software that helps in storing, citing, and collecting literature sources such as books and research papers. It is pivotal in the video's theme as it serves as the primary tool for organizing research materials. In the script, the speaker uses Zotero to manage their collection of academic papers and discusses its features like quick add, subcollections, and tags for efficient organization.

💡Obsidian

Obsidian is a note-taking and knowledge management app that allows users to create a network of connected ideas. It is central to the video's narrative as it is used in conjunction with Zotero for processing and storing information from research papers. The script describes how to set up a sync between Zotero and Obsidian and how to use it for creating literature notes and atomic idea nodes.

💡Reference Manager

A reference manager is a software tool that helps scholars and researchers organize their sources of information. In the context of the video, Zotero is highlighted as a reference manager that the speaker uses to avoid getting lost in the multitude of research papers and books. It is essential for managing citations and maintaining an organized library of sources.

💡Literature Notes

Literature notes are notes taken while reading academic papers or books, capturing key points, ideas, and insights. In the video, the speaker discusses the process of creating literature notes in Obsidian linked to sources in Zotero. These notes serve as a reading journal and a place to outline key points and personal thoughts while engaging with the material.

💡Atomic Idea Nodes

Atomic idea nodes refer to the fundamental units of thought or concepts extracted from reading material and rephrased in one's own words. The video emphasizes the creation of these nodes as part of the knowledge management process, where complex ideas from research papers are broken down and simplified for better understanding and integration into one's own thought network.

💡DOI

DOI stands for Digital Object Identifier, a unique alphanumeric string assigned to a digital document, such as a research paper, to provide a persistent link to its location on the internet. In the script, the speaker mentions using the DOI to quickly add papers to Zotero, highlighting its utility in managing digital academic resources.

💡Tags

Tags are labels used to categorize and filter items in a digital system. In the context of Zotero, as discussed in the video, tags are used to classify papers by topic or relevance, allowing for easy discovery of papers on specific subjects. The speaker uses tags like 'hippocampu', 'place cells', and 'optogenetics' to organize their research papers.

💡Subcollections

Subcollections, in Zotero, are similar to folders but allow for a paper to be part of multiple collections simultaneously. The video script describes using subcollections to organize papers by context or project, such as creating a separate collection for lab research or a presentation, enhancing the organization and retrieval of academic sources.

💡Citations

Citations are references to the sources of information used in one's work. In the video, the speaker explains the process of citing sources within Obsidian using a plugin that integrates with Zotero. This allows for easy referencing and linking of ideas back to their original sources, which is crucial for academic integrity and further exploration.

💡Research Revit

Research Revit is a tool mentioned in the video for discovering relevant research papers. The speaker describes setting up a link with Zotero so that every article added on Research Revit automatically appears in the Zotero database, streamlining the process of finding and organizing research materials.

💡Flashcards

Flashcards are a learning tool used to test recall of information, typically consisting of a question on one side and an answer on the other. In the script, the speaker suggests using flashcards based on facts from a paper as a method of post-processing and committing information to memory, which can deepen understanding and facilitate retention.

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.

Short Form赞助商提供的书籍摘要比Blinkist更全面，并包含互动练习和作者见解。

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]

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