Zettelkasten workflow for research papers | Zotero & Obsidian link
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- čas přidán 19. 05. 2024
- Shortform link:
shortform.com/artem
Plugin links:
Better BibText for Zotero:
retorque.re/zotero-better-bib...
Citations for Obsidian:
github.com/hans/obsidian-cita...
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My name is Artem, I’m a computational neuroscience student and researcher. In this video I talk about how I use Zotero together with Obsidian to efficiently turn research papers into Zettelkasten notes.
Socials:
Twitter: / artemkrsv
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OUTLINE:
00:00 Introduction
01:14 Zotero organization
05:03 Linking Zotero to Obsidian
06:48 Inserting a paper link
08:11 Literature notes
12:49 Final words
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Icons by flaticon.com
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shortform.com/artem
“Creative process, not a production pipeline.” Simply stated, gets to the core of which I constantly need to remind myself. Thanks!
Guys this guys content is very highly thought. He is not copying anyone. He is sharing what he learns and applies. Don't care about sponsors (rn at least) so very unique and very helpful. I am watching his all videos for last 2 days. Gonna finish them up soon. So even he doesn't know he is a friend of me rn :) (not bidirectional friendship or linking tho)
Subscribed on the strength of this video. The workflow between Zotero and Obsidian was particularly helpful.
Another great video, Artem! Always great to see people doing the same type of work with similar workflows, the difference being that I am a linguist and use org-roam.
Would really like to see how you use Anki and how you decide what kind of information should go into a card. This is where I'm struggling because I never know if I want to remember something.
Great video Artem. I especially like your point on not "having to do x" at the end. I feel like a lot of people in PKM/Zettelkasten get caught up feeling like they have to make lit notes, have to extract to idea note etc. We need to remember the function of these tools in the wider context.
I'd like to see the post-processing video you've been hinting at making.
Cheers.
I really enjoy your content and your approach to Zettelkasten/Obsidian! I would love more insight into your own student workflow (class notes, textbooks, etc). As a student, I've personally found it difficult to integrate Obsidian in my university coursework. Thanks again!
I personally use it mostly for studying purposes as I prefer to take notes in class by hand. Afterwards, I might create a note for each week and try to synthesize some of the main concepts and things I might not understand fully. How extensive and detailed this is depends largely on the class. If you feel like it's not going to be a benefit, don't waste the time, unless you want to be able to reference some of the ideas later down the line. In that case, simply create a zetalkasten "hub" so to speak for just the class where you can just create a bunch of detailed note ideas and definition indexes perhaps.
It's a creative process and work with the flow. That is the best advice I have heard after many Zettelkasten workflow videos. Thank you 😃
Another great video! Thanks. I can see that you came up with a practical solution for people who needs to get the job done!
Thanks, man I really appreciate your work! It was very helpful to see you apply your work/ideas in PKM
Im a posgraduate student of psichobiology and your video just helped me to organize and make structure of my mind and to motivate me in working on my thesis and future projects.
Greetings from Mexico 🥺Thank you
Hey just gotta say that your section on taking literature notes has really helped me come up with how I implement my own Zettelkasten system. I've struggled for about 2 years now understanding the relationships between fleeting notes, literature notes and permanent notes. Almost always I only wrote what I considered literature notes--basically reading the source and then in my own words writing down key points and ideas. But anytime I actually came up with an idea, I never made it a permanent note because I always thought permanent notes needed to be original thoughts and ideas; except I always knew where my ideas came from and they're from one of the thousands of "literature notes" I've been taking. Nothing ever really feels truly "original" in my mind. Like my ideas around habit formation are almost 95% sourced from Atomic Habits, so are these really my ideas are they James Clear's?
I wish I knew earlier that an "original" idea is actually more curation than creation.
I don't use Obsidian and instead have a Frankenstein of a Notion system I like to use, but I wanted to share that you really helped fixed a gigantic problem I've been struggling to solve for many years!
Nice! I think getting over the obsidian learning curve may be slightly too steep for my preferences, but it's always fun to see how others organize their intellectual habits.
Thank you for this Obsidian / academia content; it's been a total game changer!
Your video always on time 💙
I've actually needed some advices about organizing my workflow and literature notes)
You’re the best. CZcams had unsubscribed me even though I’ve watched your videos with regularity, given thumbs up to each, and have been subscribed for quite a while . FYI.
Hi, Artem.You are amazing!Thank you very much!Your approach save millions time for me !!
I've been meaning to set this up. Thanks for the tutorial!
@Artem Kirsanov your video is very helpful. I also like Vicky Zhao's "[Obsidian Template] for Zetelkasten Note Taking".
I am about to set up my own Zotero / Obsidian setup and your video convinced me to get off the fence. Thank you.
In addition to transferring to Obsidian; Zotero can write out a bibliography or reference list in numerous academic styles including those of several journals. Zotero can also connect to a writing tool such as MS Word and handle footnotes in a variety of styles.
Bibliography/Reference List -- problem solved! Love it.
BTW as a bonus, one could create an inventory of the books one personally owns in hard copy, Kindle or PDF just with a folder or tag. That's just a simple subset. Likewise Obsidian as you mentioned can serve as a personal reading journal or using time stamped notes can serve as a lab notebook -- if one needs a lab notebook for patent purposes one could sync it with GitHub. One can organize code snippets and keep them in context!
Your content is absolutely brilliant!
I have been copying and pasting references like a digital caveman. Thank you so much for this video!
Спасибо за контент! Очень интересно!
Artem, you are a king. Thanks man.
Very helpful tips. Thank you.
This is extremely helpful stuff again, thank you 🙏
Hey man very well done! I use these two plugins already daily but this is a great summary! I'm also implementing Pandoc with Obsidian and it came to mind when I saw the way you store your reference notes. Are you also using it for your own writing?
Thanks Artem for the post. I wonder if you, or anyone else, could comment on relative advantages/disadvantages of the workflow you describe in this video versus the following:
1. Read source in pdf format.
2. As you're reading, highlight quote or passage of interest.
3. Write a note (embedded in the highlighted content) in your own words processing the content.
4. Extract the annotated highlights and your processed notes using the Zotero plugin Zotfile.
5. Once extracted, export the final Zotfile note as a "create full markdown file" (with both metadata and extractions) into your Obsidian reference folder via the Mdnotes Zotero.
6. The result is an Obsidian metadata note with the citekey as the title, followed by all your highlights and process notes in one markdown file, ready for processing into permanent notes.
I 'm just setting up my system, thanks to your excellent simple Zettelkast in Obsidian video....but this part is driving me crazy. I'm worried their are major ramifications either way that I can't see right now. If you or any of your subscribers have experience with these relative options, I would be very grateful for your insight.
this is super helpful for me, thank you sir!
Very helpful video especially in getting the hang of Obsidian. Thanks. One comment: aren't 'collections' (or what you call folders) in Zotero more like a separate set of tags since something can sit in multiple collections/folders? I think using them as you do for projects while having tags for thematic areas makes a lot of sense.
Excellent video and fantastic content you a creating, Artem! I'm sharing it with colleagues and students. Please keep up the great work!
Question: how do you organize the PDFs you keep track of in Zotero?
About 2 years ago I tried using Zotero and it bothered me that it stores PDFs in a weird folder structure that would make it hard to find my papers if for some reason the Zotero DB was corrupt or missing. So I stopped using it and just keep PDFs in folders by topic, which is much less practical but makes it manageable and allows me to synch easily with OneDrive. Thanks!
Thank you, love your videos
Hi Artem, thanks a lot for making so much awesome content. Since you're a neuroscientist: Does that high-paced CZcams speaking pace really help viewers / listeners digest the information that you present? I mean that as a serious question, as I find that I learn much more when listening to Andrew Ng than when listening to CS50's David Malan, as an example.
it's uncountable the amount of time you've just saved me by showing how to integrate seamlessly zotero in obsidian.
thank you!!
btw how do you get the hyperlink toward zotero in your reference notes?
Same, can someone explain how to get the hyperlink? It does not show up for me. I only get the title, author, and year.
You can add something like [{{citekey}}]({{zoteroSelectURI}}) in the "Literature note content template" field in the Citations plugin settings.
BTW thanks for removing the mic away a bit more :) we don't have too much voice explosions thanks to this :)
thanks for the video!
Thanks Artem for this video. I am using Obsidian for past one year but could not make it my main note taking system… Could you please create a video on note taking in Obsidian for students (Engineering) alongwith the list of relevant extensions.
10:06 I really needed to hear that
Nice explanation
Definitely going to try zotero - seems there has been a plug-in created for Notion which is where I have been keeping my settle and research notes
Like your style -- it certainly clearned up a few things for me. Did you ever look into Mendeley for that same process? Reasons for/against Mendeley over Zotero?
This was everything that I was doing across multiple different resources and combining them into one! This is exactly what I needed to bring organization to my scattered thoughts. Thank you so much!
I am a 2nd year PhD student in Molecular Genetics & Cell Biology with a dual Anatomy Teaching Track - I am juggling so much between my research (pancreatic cancer cell biology) and teaching (anatomy). I have so many ideas and just feel like I dump them to random places and then forget about them. I am excited to get my obsidian set up so that I can connect my ideas.
My PI uses EndNote as a reference manager, is there a similar way to integrate EndNote into obsidian like you did here with Zotero?
As a student just getting into properly using Obsidian and only contemplating Zotero, I find your content extremely useful, precise and well-explained! Downloading random pdf's, highliting stuff in them and then forgetting is a problem of mine.
I wonder if Zotero can support ГОСТ tho, as I can't properly write it down myself and would be glad if it could....
This is awesome thanks
Amazing video, thank you so much for this. I started with your method but have since taken the dive into using Zotero Integration exclusively instead of a mix between it and the Citations Plugin. It is better overall but the effort of setting it up is probably not worth it for most people, especially since they would have to know at least basic programming to handle Nunjucks. Sidenote: Why did you censor yourself @5:34? :D
Gold! 🤩
Thank for your awesome content! I wonder how you custom the title, authors and year on the header section in 9:38 ?
Thank you - how do you show the green tick tag or fire tag on the list of papers at 5.01?
This is exactly the video that I have been searching for having just finished reading "How to Take Smart Notes" by Sonke Ahrens, and I am trying to implement the literature notes piece in Zotero, before moving on to my Obsidian setup.
I have a question. Ahrens suggests using Zotero to collect the references and notes that you take during reading (p29 of 2nd edition). Your workflow seems to be using Zotero to collect the reference only, and you are maintaining your reading notes over in Obsidian. Was Obsidian linking the reason that you chose this approach?
How did you incorporate the "See in Zotero" link into your reference notes?
Hello Artem,
your videos are a huge help, especially for a beginner like me. I used to have a manual structure with a Literature Notes folder in which I simply note key points from my Zotero File opened on a second monitor, using the latter mainly to highlight text in different colours. Then I used to simply link the PDF into the header of my note and add tags and topic notes ( like: #PrimaryRead #Theory [[Behaviour]] [[UX]] ).
Does it make sense in your opinion to keep the citations generated files as they are, or could I also utilize them as my actual Literature Notes as well. This way a reference in a note would lead me directly to the meta data AND my own notes, good or bad?
Cheers!
EDIT: I should have watched further, you basically do so with your Keypoints. So, where would be the difference to the traditional idea of a separate Literature notes folder, or is there none?
OMG THANK YOU!!!!
thank you so much
Thank you for this video! But how do you create the "See in Zotero" link in the reference note?
I love this Vim vs Emacs comment! Truth.
thank you for this video. I found it very helpful. I am curious, do you take notes in Zotero or directly into Obsidian while reading the article in Zotero?
Thanks for the timely video! I’m getting started with Obsidian and am in the middle of transitioning away from Papers 3 for Mac now that it has been EOL’ed and won’t install on my new iPad. The ReadCube Papers app that replaced it is pretty awful.
There’s a lot I like about Zotero, but how do you get by with the non-native UI (its very Java-y) and lack of Mac features (QuickLook, etc.)? Do you use an app to access your Zotero library on an iPad for reading and highlighting?
I actually don't mind the UI, for some reason it looks great to my eye :)
Maybe, this has to do with the fact, that I’m using Zotero beta ( www.zotero.org/support/dev_builds ), idk
If you’re on Mac and if you’re using Alfred, there is a great Alfred workflow for Zotero to search your library ( github.com/deanishe/zothero )
For the iPad, there is also a Zotero application, which is still in beta and can be installed using TestFlight. You can sign up for mobile beta testing here: www.zotero.org/support/mobile
Another approach, which I’m transitioning to at the moment, is to store all your Zotero attachments on cloud storage (I went with Google Drive). Then you can open the pdfs and edit them in any application on IPad / phone. This article may help to set it up:
medium.com/@hasal98fernando/use-google-drive-to-store-pdfs-with-zotero-in-3-steps-c36135d53f86
Hi, thank you so much for your video. Please, how did you add those tags like the fire and green check mark buttons ? Thanks !
❤nice video ! Can I use zotero to prepare for final exams ?if yes ,how?
Hey Artem! New to Obsidian and Video Making - how do you make those trnansitions in the video? :)
How do you change the header of your literature note? Do you use a template or do you do it manually?
Thanks so much for the wisdom of your content! Game changer in time management/productivity. I'm very new to obsidian and having a problem with one of the parts of your video. Is there a correct way to copy the JSON file of your zotero references into the citation settings in obsidian? Whenever I try and copy it over I get told that 'the citation export file cannot be found. Please check the path above.' Thanks again for the content :)!
DW! figured it out, had to hold the option key to copy the path of the file and not just the name! Beginner gains haha
@@nickyg5389 Thanks for this! was confused on my end too
This is great, Artem! Do you highlight or mark up the PDFs of your research papers? If so, what's your workflow of getting these into Obsidian? What's your workflow for getting diagrams and graphs from papers into Obsidian? Thank you!
Thanks!
I do highlight the paper, when I'm reading it, but I don't export these highlights. They are temporary, so that it's easier to extract key ideas.
I then rewrite important things in my own words in Obsidian. Diagrams and graphs are usually inserted as images into the note (I just take the screenshot of that portion of the paper)
@@ArtemKirsanov Thanks, that's helpful. Another quick question: do you find that the empty citation notes from Zotero clog up your graph view? Or is it easy enough to filter out the ones that haven't been used.
My Zotero database is a conglomeration of references that I've collected in various contexts over 10 years . . . I love the idea of the method that you're describing but don't want too much out of date stuff to end up in Obsidian.
@@drmelhopperkoppelmandac6834 The plugin does not automatically create a reference note for every paper in the database. It just provides you an ability to create a note with all the metadata in one click. For the reference note to exist, you'll have to explicitly tell Obsidian to create such a literature note. So, don't worry ;)
Plus, even if you create a ton of reference notes and you don't want them to show in the Graph view, you can filter the graph to include notes only from specified folders (gear icon in the top left corner of the graph view) and hence exclude all of the references
@@ArtemKirsanov Amazing! Thank you, that's so helpful
Thanks so much for tNice tutorials bro
Hey, thanks for the fantastic guide! I got everything mostly set up - but I noticed that my resulting references in Obsidian look a bit different - they only show the top part of the reference (seen in your video at 7:54). Does anyone know how to get the "See in Zotero" link to appear?
In Obsidian under Citations settings, scroll down to "Literature note templates" section, in the box next to "Literature note content template" leave what is currently there and add to the end:
## {{title}}
[See in Zotero]({{zoteroSelectURI}})
And this will now do exactly what his does when you add a new Literature note link and click on it,
Idk why he left this out of this video but it drove me crazy to not be able to have the same functionality. Otherwise a great video.
Note: have Zotero already opened in the background *before* clicking "See in Zotero" link, otherwise it won't load properly if Obsidian tries to open Zotero itself (at least for me it didn't)
I get error message: Unable to access literature note. Please check that the literature note folder exists, or update the Citations plugin settings. Anyone have an idea what is happening? I checked the path to Reading Notes. The plugin does not provide a way to identify the path to the template.
thanks!
Super helpful video! Thanks. Can you tell me how to make colored tags (a tick in a green window, for example) like in your video?
Thanks! It's the plugin for Obsidian called Admonition: github.com/valentine195/obsidian-admonition
Is this what you are talking about?
hello Artem! Huge thanks for this content. I personally am trying to figure out which way to go, so got curious what decision did you make on this; do you think getting unlimited storage on Zotero is more sensible than using Zotfile/OneDrive combo for storing files etc? How did you sort that out in your case I'm wondering, if you dint mind me please? best x
Hi! Thank you!
I personally went with external storage (Zotfile + Google Drive) mainly because I wanted to highlight pdfs as I'm reading them and save the highlights / annotations / notes for later in the same file. So that I can access them in other applications (like Acrobat / Notability) or share the highlighted version.
Whereas if you read in Zotero itself (and I really like their inbuilt pdf viewer by the way) highlights are only saved within the Zotero and not embedded in the actual pdf.
But other than that, it's completely up to you! ;)
@@ArtemKirsanov I completely can understand as a fellow phd candidate dealing with massive pieces of information and data- when it comes to keeping notes as you read. Your way of managing readings sound more secure and quickly reachable- will probably go along with OneDrive as it is accommodated by my uni. I just wanted to make a 'safer' choice discussing first with you as you're the one with more experience. And very much appreciate your swift response too! best wishes in your studies! x
thanks your sharing ,but i suffer a question. When i cite some contents from zotero at obsidian, only the abstract cannot produce automatically.
1. how did you re-order the information pane for the items to show up on the bottom>?
so I wasn't able to insert the citation, even though I could search through them - & then noticed I still have to create a folder in your vault named "Reference notes" so the notes have a place to go.
Tip for noobs like me.
Hi, thanks for the super helpful content. One thing I am still struggling with is how to deal with citations inside research papers: If for example I read a review, most of the points in the review paper are not original but distilled from other papers. How do you deal with that, do you write down the idea in the reading note, mentioning that it´s cited from X or do you go to X and try to get your own conclusions? This at least would make reading reviews obsolete haha
I have the exact same question. Been waiting for a response.
Thanks for this helpful video! You mentioned a tool for finding relevent paper, but it seems to me there's no video attached. What is that software/website?
Hm, must be a problem with CZcams cards. Anyway, I was talking about ResearchRabbit ( researchrabbitapp.com/ )
Here's the video I made about this tool, but it could be a bit outdated, since there has been a number of updates, since the video was released
czcams.com/video/Z9C4mPR0uI4/video.html
Great video! How do I make the "See in Zotero" hyperlink? I can't figure it out.
Thanks!
In Obsidian, go to Settings -> Plugin options -> Citations and scroll to the field "Literature note content template". There you can configure the template of the reference note. I have mine set up as:
---
title: "{{title}}"
authors: {{authorString}}
year: {{year}}
---
# {{title}}
[See in Zotero]({{zoteroSelectURI}})
That should work ;)
Is there.... a way to use the Tags from zotero to sync them with tags in obsidian? I haven't been able to find it.. and when I look at the .json there's no class of 'tag'
I had a question: what do you write in bibliographic notes that start with an @? Or do you not write anything and they only serve to see the links of the notes linked to them? Are these chapters that appear at 9:47 from a note or from the reference note that was created by the plugin and you wrote all of this in it?
Hey Thank you for the video! I followed all your steps but as soon as im trying to insert the Zotero reference, their reference link doesn't show up. do you have any idea why ? thx!
Notes:
1. Use the magic wand and paste DOI
2. Zotero Connector web extension for PDFs
3. Better Bibtex plugin for Zotero
4. Citations plugin for Obsdian
5. Ctrl + shift + E (or search (cmd+P): "citations"): insert literature note link
Zettelkasten workflow:
1. Use literature notes as a reading journal: outline key points as you read
2. Graph view in obsidian: visual atomic summary of an article (which links to zettels)
3. Flashcards stored in literature notes for space repetition
4. Mindmaps in literature notes
*As this is a creative process, there are no "must-dos," be it post-processing, or just taking notes. Go with the flow.
Keep going please
This motivated me to finally try Zotero. How do you add the 🔥✅ to the title?
I think, Zotero does that if you first create an emoji tag, then in the tags pane (bottom left corner) click on it, select "Assign color" and then select any color from the list. This should do the trick
@@ArtemKirsanov Hmm, nope, I see the colored square, but not the emoji itself. Are you using version 5, and do you have any other add-ons installed?
@@xl0xl0xl0 I'm using the version 5.0.97-beta.64, so maybe it's the beta-only feature. You can find Zotero Beta here (but be careful, since it's not fully stable) www.zotero.org/support/dev_builds
@@ArtemKirsanov Yeep, that was it! Thanks a lot!
@@ArtemKirsanov Thanks for sharing. I hope you can PLEASE respond to my question about how to enjoy reading research papers faster and mkre enjoyable and also how not to get bored and stressed in grad school. Thanks and hope to hear from you.
At 6:35 'if everything ok"... But what if everything isn't ok? When I enter the file path, the following message appears in red: "the citation export file cannot be found. Please check the path above." What to do to resolve this problem? Amazing video!
Hello Artem , I am trying to extract all my notes and Anotations from Zotero at once, any suggestions for this ?
Hey!
My Literature note content template just says on default:
---
title: {{title}}
authors: {{authorString}}
year: {{year}}
---
Could you post yours here? :)
How do i make Obsidian create the link "Open in Zotero"?
How did you make the emojis colorful in Zotero? For me they stay white and black.
Are you still using the Citations plugin or have you changed to Zotero Integration?
How do I get those emoji tags to show in front of the paper title like it does in the video?
when he references the zotero citation in obsidian theres a pop up there where he can open up the PDF in zotero... how does one do that?
Me watching this only having a high school degree, haha
Does the obsidian/citation plug in create the template or did you do that?
Looks like Obsidian/Citation creates reference cards!
Cool!
Getting the reference right the first time with just and ISBN for books is amazing.
А как Вы думаете, как наилучшим способом организовать работу с Обсидианом и Зотеро, когда приходиться работать на разных компьютерах плю с телефон еще? Как синхронизировать заметки между машинами? Или ничего не выйдет?
And what do you think is the best way to organize work with Obsidian and Zotero, when you have to work on different computers, plus from a phone? How to sync notes between machines? Or nothing will come of it?
How do you add emojis as tags?
How do you get emoji as tags?
It looks that citations plugin in Obsidian is just not being supported any longer, right? Does it keep working for you guys?
Citations path - the Citations export file could not be found. Please check the path. I just went to icloud and copied the path to Zotero/*.json file and I keep getting the same error. Anyone have a clue?
10:07 ayy shoutout atomic habits
Did you ever face the problem that interface panels in obsidian become bizarrely enlarged and you can't reduce them?
Have you used the Zotero Integration Plugin yet?
can I know how you get that green checklist and fire logo in zotero?
It's a feature of Zotero Beta, which you can find right here www.zotero.org/support/dev_builds (but be careful, since it's not really stable)
In Beta, if you first create an emoji tag, and in the tags pane (bottom left corner) click on it, select "Assign color" and then select any color from the list.
This should do the trick
@@ArtemKirsanov I get it thanks! I assume that you put the emojis into the tags section of the paper and after you're done reading it, you remove it manually?
I don't know why I can't successfully insert the link in my obsidian. I just failed in the final step TT