Obsidian Zotero Integration Plugin | Streamline Your Research Paper Workflow 📝️
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- Опубликовано: 20 июл 2024
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Want to get your hands on my Obsidian templates, Custom CSS, and Mermaid Diagram code? 👉🏻️bryanjenkstech.ck.page/d4ec07...
0:00:00 Welcome
0:00:27 • Writing with Zotero an...
0:00:44 Getting Setup
0:01:31 github.com/retorquere/zotero-...
0:02:01 Configuring the Obsidian Zotero Inegration Plugin Settings
0:06:22 Thor decideds to help with video production
0:08:25 jinja.palletsprojects.com/en/...
0:08:43 Wrapping up the Setup Process
0:09:00 What does my markdown template look like
0:12:19 Thor decideds to help with video production
0:14:22 jinja.palletsprojects.com/en/...
0:14:39 Wrapping up the Setup Process
0:14:57 What does my markdown template look like
0:16:19 The workflow that is using the template
0:20:24 Related paper linkages
0:20:51 Inserting citation using the plugin
0:22:16 The workflow that is using the template
0:22:48 Linking citations using Obsidian Hard Links
0:23:46 Random Tangent about dataview metadata and linking to future papers automatically
0:29:43 End random tangent
0:33:14 Wrapping Up
0:35:32 Sticky Flags - amzn.to/3WnSQY2
0:35:34 Highlighters - amzn.to/41Z8laj
0:36:28 / discord
0:36:34 Outro 
Наука
Want to get your hands on my Obsidian templates, Custom CSS, and Mermaid Diagram code? 👉🏻bryanjenkstech.ck.page/d4ec0713d5
0:00:00 Welcome
0:00:27 ruclips.net/video/CGGeMrtyjBI/видео.html
0:00:44 Getting Setup
0:01:31 github.com/retorquere/zotero-better-bibtex/releases
0:02:01 Configuring the Obsidian Zotero Inegration Plugin Settings
0:06:22 Thor decideds to help with video production
0:08:25 jinja.palletsprojects.com/en/3.1.x/templates/
0:08:43 Wrapping up the Setup Process
0:09:00 What does my markdown template look like
0:12:19 Thor decideds to help with video production
0:14:22 jinja.palletsprojects.com/en/3.1.x/templates/
0:14:39 Wrapping up the Setup Process
0:14:57 What does my markdown template look like
0:16:19 The workflow that is using the template
0:20:24 Related paper linkages
0:20:51 Inserting citation using the plugin
0:22:16 The workflow that is using the template
0:22:48 Linking citations using Obsidian Hard Links
0:23:46 Random Tangent about dataview metadata and linking to future papers automatically
0:29:43 End random tangent
0:33:14 Wrapping Up
0:35:32 Sticky Flags - amzn.to/3WnSQY2
0:35:34 Highlighters - amzn.to/41Z8laj
0:36:28 discord.gg/MxCVshN
0:36:34 Outro
Doesn't seem to work anymore, it just says "TypeError: NetworkError when attempting to fetch resource." when clicking "Yes please"
I learn so much from your videos. So helpful! I've been looking into Zotero for a while and didn't think it would integrate well enough with obsidian until seeing this integration. Still on the fence but it's a top contender for the graduate work I'll be doing soon. I also appreciate seeing how your notes for books impacts your Zotero and Obsidian workflows. I'll be adopting some of those practices!
Glad you got some value from the videos!
I love your videos especially when you go straight into the action
glad you enjoyed it!
This video deserves soooo much more comments and likes and views!!! It is insaaane!! Thank you very much for going step by step with us!!
thank you! glad you enjoyed it!
Thanks for another superb video. Glad to see you back.
More to come!
What a great video, I spent a whole day configuring it, but I managed to customize my template, excellent method for researchers. thank you very much, greetings from Colombia!!!!
Glad you enjoyed it!
Glad the video helped 😁
Zotero + Obsidian for the win!!
Thanks again man!
@@BryanJenks Got one coming out this week about metadata menu and wow - it is gonna be long but goooood!
Can't thank you enough for doing this video! Subbed!
Welcome!
Thank you very much for this video. It’s tremendously helpful.
Keep up the good work.
Glad it was helpful!
You're back with another video to delve into!
Indeed I am!
Thanks for the great video and thank you Thor for weighing in!
Haha you’re welcome!
Excellent. Thanks. I needed this instruction.
Glad it was helpful!
Nice video! I'm struggling to get all this setup for my workflow, and this has helped a lot! 🐄
Glad it helped!
Excellent - especially for the related items.
Glad you enjoyed it!
Great video and super helpful. Finally able to get the linkage working after trying so many other's directions. Would you please provide a link to your new, updated Zotero Paper Template? I have the existing one from 2022 you provide but I like how you created this version. Thanks!
Shoot me an email, template vault isnt updated yet
Fantastic video. I am a current graduate student and I was literally looking for content on how to use Obsidian for the first this week. This was such a motivating introduction.
Is there any chance that the template that you've set up on the video will be available for download in the future? Especially considering all the plugins and necessary steps to make it work (for someone starting from scratch, like myself?)
Any other videos of yours that you'd recommend for someone in a similar situation?
Best regards.
working on it right now, but go ahead and email me and i'll get you an advanced copy so your studies are not affected ✅
@@BryanJenks Hello, I am currently attempting to replicate this template for my own research as an upperclassman student in university. Is this template currently available for download?
Thanks for sharing your work flow ❤❤❤
My pleasure!
Thank you thank you! Great tutorial
Glad it was helpful!
This is really a fantastic video! Thank you for the explanation. It looks like a great plugin. I've just started using Obsidian and Zotero. I used to take reading notes with Word before, which was cumbersome and not easy to search. I want to know if it's possible to put notes from many articles into one md document by this plugin? Thanks again for your guidance.
glad it was helpful!
Bryan thank you very much for your videos, the recommendations and academic settings have been very useful for my research work. This video is amazing and very useful. One question do you use Zotero with local storage or in some cloud like Drive, have you tried having the Zotero file folder in the cloud or does it malfunction?
I use zotero storage which syncs to the cloud but hosts locally and have had no issues with it
@@BryanJenks Thanks Bryan, in which cloud do you sync Zotero?
Zotero has a cloud host service it’s just part of having a zotero account
18:20 Are you sure it pulls everything? Because I don't think it does.
In the PDF viewer, all the highlights and notes in the left are annotations. However, whatever is in the right pane is in a note.
- Using the Import paper (Set up via Import Format), will only import the PDF annotations (from the left pane).
- If you want to actually import your note from Zotero, you have to use the Import Notes.
ah, probably missed that as i dont use the notes feature in Zotero at all so this is good info!
Hey Bryan, I just found your channel, and I'm absolutely obsessed! Would you be able to share what the emoji tags in your Zotero represent? I would love to adopt them as part of my Zotero workflow as well.
ive gone over it several times in my zotero videos :) check the playlist!
l love your workflow! Thanks!
Glad you enjoy it!
Thanks for all your work and publishing this out. I am running into an issue when papers have colons in the title. Is there a way to replace the colons in the title to a dash in these situations and still use your renaming method? Thanks!
yeah, likely something to do with this: jinja.palletsprojects.com/en/3.0.x/templates/#jinja-filters.replace
This is awesome! Thank you for sharing your process in such detail. Do you have the template available somewhere? Thanks in advance.
if you email me i'll send it that way, its out out yet
Thank you so much for this valuable insight to your workflow!
Do the zotero items imported in Obsidian automatically update when you change the items in Zotero?
I am looking for a very simple workflow with Obsidian + Zotero + Word where I simply collect sources from the web and reference them in my notes in Obsidian. In the end I want to write my master thesis in Word and be able to transfer portions of my notes including the references WITHOUT having to update the links to Zotero in order to keep them synced. Is this achievable? How would you go about this?
they do not, there is no bi-directional sync, there is just export of content to obsidian
Amazing video! Looking forward for a template
Coming soon!
Thank you for the video!
When I used 'Shift + option + Y' and a new document is created. With few references the top part of the created new document is in red font. Would you know why this might be so?
I need visuals to better understand, try my FAQ repo on GitHub
Was just busting my head trying to figure this workflow out :'). very timely. By the way, bit of a basic query, but how do we extract and incorporate your Obsidian custom themes and templates from the newsletter mail you send to us? Seems really fanastic, thank you very much!
the newsletter package is a whole template vault setup and configured, but ill be working on it soon to polish up the instructions, as it stands the template i showed in this video is not currently available at the immediate moment
@@BryanJenks A set of instructions would be greatly helpful, thank you for all that you do!
@@BryanJenks Will you send out a newsletter when the updated template is available? This is amazing and I would love to try it for myself! I'm new to Obsidian and I feel like I'm missing some of the aspects of your setup.
Hi, Thank you so much for this workflow! I'm having trouble getting the highlighted colors on Obsidian. They are all just uniformly a light brown shade. Also, how do I get the non-.md files like 'publish.css' from your starter_vault onto my Obsidian vault?
i used the hilightr plugin for the custom highlight colors combined with some CSS, i have a video coming in a few weeks that will walk through the whole setup and configuration of every plugin and setting for this workflow in detail
for publish.css you can just drag that to the root of your own project in the file explorer
Hi Bryan, are those templates are available in your public vault? or how do we integrate this new workflow into your old vault and templates? Thanks again for cracking zotero workflow. And the black theme for zotero? How can I find that ;) 😬
still working on getting the template out there, at present its only in my personal vault. Black theme in zotero is from this repo:
github.com/Rosmaninho/Zotero-Dark-Theme
but this one is also available:
github.com/tefkah/zotero-night
@@BryanJenks Got the dark mode. Thanks! However, could not manage force OS dark mode to get dark titlebar and white text color. Any idea where precisely to add key and string to the Info.plist file in zotero?
Hi Bryan. Thank you so much for a great video. I'm new to obsidian and zotero and I'm learning everything from scratch. I subscribed your newsletter and got your template but seems to be outdated. I'd super appreciate if the template you used in the video is avalible some where. Thanks!
Email me, I still haven’t gotten around to updating that vault yet
Hi Bryan,
Thank you for this very helpful video! I really appreciate it as I believe it will help me streamline my research process. Question for you - I've run into an issue where sometimes the PDF annotations from Zotero will not populate into Obsidian, depending on the PDF. It works for some papers, but not for others. Do you have any advice for this issue? Thank you!
With just that context no I have no idea, are you using the template exactly as I had it? Are you replicating my workflow exactly as I do it? There’s a lot of variation possible that makes this difficult to troubleshoot.
Thanks so much this is genuinely the best work flow additive ive had in a while. I tried getting your templates from the link you posted, but its giveing a network error. how do I get these pretty templates of yours?
Email newsletter signup or GitHub sponsorship for the cutting edge :)
Beautiful, beautiful tutorial. What theme are you using? Looks very good
Gruvbox with a lot of custom code :)
Thanks for sharing this! Would love to get the template that you're using in this video if possible
Sent you an email :)
Hey Bryan, great video! I've used your template, but when I highlight text, either in purple or blue, on Zotero it is imported blue on Obsidian, do you know how to fix this (i.e. how to import the purple as purple)? thank you very much!
not sure how thats happening to you. i'd need a lot more information to figure out why this is happening
hello!
do you know if there is a way to add in the author(s) name and publication year prior to the annotation page link? (basically a parenthetical citation)
thank you so much for your videos!
I'd have to spend time to look up the syntax but i think thats a pretty easy thing to do with the template syntax used by the plugin, yes
Hi Bryan, I really like your approach as to renaming the note by adding some static information/date to the citationkey. Could it be that this limits any future updates to that specific Zotero-item upon re-importing? Re-importing the same Zotero-item after having made additional annotations thereto, seem to result in a templater-error message (potential upon renaming; item already exists) and hence, the updated item is saved as a duplicate with solely the citationkey as title (default setting). Figuring out any work-around.
I don’t re-import so that’s a non issue for me, I usually just read the paper and export notes once
@@BryanJenks Thanks for taking the time to respond - much appreciated. For those who want to update after import, a potential work-around would be to add the date into the citation key.
Very useful video. I followed your instructions but in obsidian i am not retrieving data. I have already tried reinstalling Zotero integration Plugin in Obsidian and Better BibTex in Zotero but cant make any import.
without screenshots im not really going to be able to understand or help,
github.com/BryanJenksCommunity/FAQ/discussions
Sorry for the barrage of questions... I saw that if I re-import my paper then my notes (not annotations) were overwritten. Is there a way to e.g. isolate a certain section to be not overwritten?
short answer no not that i know of
Thanks for the great video :)
I am currently using the citations plugin. Even though its functionality is much more limited than the Zotero Integration plugin it has one feature which I miss in the Zotero Integration plugin: I also take my additional notes about the reference in the obsidian note that I create using the plugin. If I then accidentally import the reference again, the Zotero integration plugin doesn't check whether the note with that citekey might already exist but just replaces it completely, so all my additional notes are lost. This is nice if you have new annotations to import but for my workflow, this is really suboptimal. Do you have any experience with this behavior?
i only import once so your milage may vary with the workflow in that case
You can use the following:
{% persist "notes" %}
{% endpersist %}
@@lucky_EINS thanks!!
Use manual backups (git) and the one included in Obsidian to return the file.
Hi, when you do any changes in zotero like higlighting anything new for example it is automatically updated into Obsidian? Do you know if there is any way to do it?
Thanks
no, there is not a live sync between the two and i know of no way to do this
Thanks, I have a new vision of this plugin functionality.
I have a question. Let's say at day 1 I imported my highlights. Then I modified generated file - added my new notes to imported highlights.
Then, at day 2, I decided to import them again (in the same file). Will I loose my notes in MD file?
Yes, that's the reason this is actually no solution for me... Thought there would finally be an alternative to Citavi…
@@wirsindsuperstars there is a solution - you may have links to the generated MD files as your thoughts.
Though it's not that convenient, of cause
Yes, correct, i only export once so this isnt a deal breaker for me
Hello Bryan Jenks, this video was really helpful. Thank you very much!
I noticed during testing that your html snippet (visible at 14:49) is prone to an injection-attack (by yourself). If "{{annotation.annotatedText}}" contains something like: "1 < 2" it is going to break your code, since "
the html characters might break formatting, but its not running anything that is executing based on extracted annotation content i personally highlight in my papers. so there's not really a risk of anything, i just replace those characters when i notice them with the HTML escape code text as you saw me do in the video ✅
@@BryanJenks Thank you for that clarification. I must have missed the part at 30:50 where you fixed it for yourself the first time. I'm sorry for that.
However in the meantime, I have found an optimised solution for myself that I'd like to share. I just found an "escape" filter for special html characters inside of the Nunjucks documentation. This filter automates the exchange of chars pre-rendering, which is really a blessing. So my code looks like this now: "{{annotation.annotatedText | escape}}". It works like a charm; no further templates needed.
Rad! Gonna incorporate that
Thanks for the “Paper” template, However, for ‘report’ zotero item type, this template does not work, it cannot rename the filename properly. Why only the ‘report’ item type from zotero does not work, while other item type from zotero works?
Report item type?
What is the title of the item you’re trying to export?
Amazing video! I have one question. It seem like this code from the template disappears when importing a paper:
When I import a paper using the template these lines of code do not disappear. Why? What am I doing wrong? :)
that is the intended function, i explain in the video that i use that to change the title of the paper after the fact so when the paper is given the initial title of the citation key, all references to that paper in other notes identify "oh that note exists now, there it is!" and the link becomes active, then the code renames the note to the correct format i want and because obsidian updates the linked references, all references to that note then update accordingly.
Hello Bryan, I need your help regarding one use case fore zotero and obsidian. Iwant to kbow if it is applicable? Any help would be appreciated.
Suppose I was gathering informations for writing introduction amd discussion sections of a paper. I labeled half of the highlight colors to resemble some subsections in introductions and the other half to resemble some subsections of the discussion. Then, I read for example 20 papers and snapped ideas the will be written in either introduction or discussion. Is there any way to export the annotations of all annotated papers sinultaneously in one obsidian note, so that for example, all yello highlights resembles the facts that will be written in one section of the intro, gathered from differet papers,each is referenced by its citation key. I think this will make paraphrasing , creating a flow, and finalize my writting a lot easier, especially if I was writting a review article or meta analysis.
I hope you get my point and I am waiting for your feedback.
yes, that is possible with modular templater tempaltes and the jinja syntax to filter out comments by a particular color if you were so inclined, so yes that is ultimately possible
@@BryanJenks I will try my best to understand and apply this as I shifted to zotero and obsidian recently. Still beginner🤣🤣.
Thank you for your help.
Maybe I didn't see in your videos, but how do you transfer what you wrote in Word? Thnx.
I don’t use Word?
What style do you use for Obsidian? Its amazing!!!
Gruvbox!
Hello. Great video, great stuff. Can you please name the obsidian theme you use? Appreciated it!
Gruvbox with a lot of customization
Hello- I realize this video is a few months old and something might have changed, but I can't get my annotations out of Zotero into obsidian. The images I select with the box tool come over but nothing else. Any help would be appreciated. Thank you for the content
everything still works exactly as it did in the video for me, so i dont believe anythings changed
Thank you- I got it to work, it was a template problem on my end.
@@BryanJenks
Super ignorant question?:
If i add some further thoughts into the imported, created by template file and then re-import the document from zotero later on; all my added lines will be deleted, right? :D
correct :)
is there a way to keep my written notes in obsidian after reimporting the paper using the plugin ?
Mmmm I don’t think so
Hi! This is still not working for me :(
When I use mdnotes in Zotero, regardless of whether I choose "Export to Markdown", "Batch export" "create mdnotes file" or "create a standalone note", it prompts me to save in the target folder (my inbox folder "0_Inbox") but when I click save, it doesn't save anything. No mdnote appears either under the Zotero entry or in my Obsidian vault.
This worked for me previously before upgrading to a new MacBook - but I'm at a complete loss now as to how to go forward!
If you’re using the integration plugin you will still need a template file, and this does not utilize mdnotes anymore
@@BryanJenks Great. I realise that was basically what this video was about. Thanks!
How do you make the link to the in-text citation from Zotero?
part of the template
Is there a way to sync Kindle books and Google books with Zotero?
sync them? i dont think so?
as someone who is using obsidian for the first time today it was impossible to follow along what you were doing. Can you recommend and other videos that might get me to the point where this one is starting out?
perhaps my comprehensive videos latest one was 2021 comprehensive but its still very relevant
@@BryanJenks I will check that one out, thanks!
Hi Bryan,
Glade to ear about this new plugin, which looks quite promising, and might replace the unstable BibNotes plugin I use for my zotero to obsidian workflow.
One question I still ask myself is: is this plugin allow you to sync annotations updates from zotero ? How you manage that ?
Also, is there a way to sync and entire folder from zotero, or only one file at the time ?
Regards,
Charles C.
this is not a bi-directional sync, it just going into obsidian, i did a proof of concept workflow on successive exports from zotero into obsidian so you can export more notes of the same paper into into an obisidan note for that paper but it is not a workflow ive polished as i do not use it
Thanks for the clarification. So you rather export new notes each time you make changes to your zotero document. If I may ask, once the note is exported to obsidian, do you tend to work within it (reflexions, summary, ...), or mainly leave it as it is? Btw, thanks for your helpfull video.
I usually work on it in zotero, export to obsidian then do some more work with it in obsidian and that’s the summary version
I see in the comments that you are still working on getting the template 'out there'. Any chance you could share it via e-mail like you did already with other people?
sure thing, just shoot me an email
Thanks for the video. I'm tryinmg to implementt his workflow, but having issues with the import of the notes and hilightr stuff. Could you please provide the template?
specifically I keep getting the error:
Error parsing template
"Bases/Templates/New Zotero Note.md":
(unknown path)
parself: expected elif, else, or endif, got end of file
try using the updated templates if youre using my sponsored vault
Thanks!
Thank you for the support!
which is the best device to run obsidian? is it possible to use obsidian in android tablet for long term?
there's no answer to that question. the best device depends on use case, what you have/can afford, what you will use, etc. answer is a giant "it depends"
never used an android tablet so i dont know. i prefer usage via desktop personally
i cant make the conections with template. Obsidian doesnt recognize it. How can i fix this?
Check the plug-in settings
When I try to add my zotero citation into obsidian, I receive an error message that states: error retrieving item data: unexpected end of json input. Any tips on what could be causing the issue and how to rectify it? Thanks
not sure, i just tested with the latest versions of everything and i have no issues
could you resolve it? i'm having the same problem
Thanks for the great video. I had this workflow setup and working very nicely for several weeks, but has just stopped working the past couple of days (no updates). Total mystery. Happened to anyone else, and if so have you found a solution? (I've tried uninstalling and reinstalling everything.)
odd. i used the workflow just yesterday with no issues 🤷🏻♂️️
Same here - but it still works on my macbook. I tried it out on my windows computer, the import function doesn't work. Let me know if you figure it out.
@@vic1269 The issue is with the new version of BetterBibTeX, so uninstall it and and install an earlier version. Some have found version 6.7.96 works for them, but I had to go older and use 6.7.94.
@@JimGrange. Thanks for the update. I saw there was a newer version (v6.7.104), it ended up working again.
Thanks for this Bryan. Can you share your template?
They’re all available via my newsletter signup
I'm wondering how to link the specific page on zotero pdf as in the video 15:33
they're automatically generated and it may be a bit unwieldy to do it manually but it is a link based on where the file is stored on your device in the zotero files
Love
🥰
where to save the better json file to keep it updated?
when did i mention json?
thats why i keep making zotero videos, things keep updating and changing and therefor breaking prior workflows 😅️
Sooooo where does one get your paper template? :D
by signing up to my email newsletter :)
When having the references, the metadata, the annotations and the notes in Zotero, why is everything imported into Obsidian. I understand why the annotations and notes should go in there, so they can be worked as notes. But all of the metadata etc. It seems like duplication. Would a simple link to your references in Zotero. I am very new to Obsidian workflow and I am trying to implement a Zettelkasten system, so there is probably a lot I do not understand :)
Sure zotero can do metadata as well but by putting the metadata in obsidian and using the data view plug-in I can basically search a whole “pseudo database” of metadata from all types of media in one place
Thor is sassy! 😼
oh he's a chatterbox for sure
🐄
🐄
Hey Bryan, I loved this wonderful demo. Just sent you an email asking to please please please share the template with me... it would be really helpful 😬😬
👍🏻
LOL "poor adhd advice" is several whole vibes
I was going to make a salty video about all the poor ADHD advice comments I get on RUclips but I figured that would be a little too negative Nancy of me and I should not be so agro about it on the internet 🤣😅
I cant get it to work
Sorry to hear that
@@BryanJenks I set up everything but when I try to import the notes all I get is a blank note with just the title. I don't know what I'm doing wrong
Could you please send me a copy of template? thanks!
its available in my template vault now
I had implemented this workflow you did here:
ruclips.net/video/mMpVMuGBGe8/видео.html
But this latest one is smoky hot, fast and more automated so I'm jumping right into it!
Thank you
glad you enjoy it! its the new hotness!
@@BryanJenks
Please where can I get a copy of your paper templates with the whole custom codes🙏
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