Comprehensive Obsidian & Zotero Workflow For Zettelkasten & Evergreen Notes 📝

[@BryanJenks]

Want to get your hands on my Obsidian templates, Custom CSS, and Mermaid Diagram code? 👉🏻️bryanjenkstech.ck.page/d4ec0713d5 00:00 Intro 00:11 Premise 02:51 forum.obsidian.md/t/zotero-best-practices/164/57 04:05 Start with installing Zotero 04:55 Downloading a Research Paper with Zotero 05:32 Downloading a paper with the chrome extention 08:18 Installing a paper with a DOI 09:32 Getting the Extentions setup in zotero 10:17 github.com/tallguyjenks?tab=stars&q=&q=zotero 10:45 Downloading the plugin files 11:32 Installing the Plugins 12:09 The Workflow in action 14:20 Zotfile to extract annotations 15:08 MDNotes for the conversion of Rich Text format to Markdown notes 15:51 Getting the markdown notes into Obsidian 17:10 The Zotero URI to the document source 17:30 Opening a link to an exact note location in the pdf source 18:17 Zotero URI links similar to Obsidian URI links 19:43 Why i enjoy this workflow 21:11 Zot Hero with Alfred App on MacOS 22:47 Closing 23:29 Outro

[@achilleskaysen9179]

instablaster...

[@momotahmasbi]

I'm thinking of doing my PhD just because of this video!

[@BryanJenks]

That's awesome! I'm glad you enjoyed the video so much :)

[@vegetaiv9275]

Thank you so much for your super helpful instruction about the smooth workflow between Zotero and Obsidian. This is the best presentation I have seen so far on KZbin.

[@BryanJenks]

thank you! check out the latest up to date version that is more accurate :)

[@b.d.m.a.9325]

This is AWESOME! I love this workflow, I'm a physics bachelor and this will be a total lifesaver 💜 at last having a neat academic database, can't thank you enough! Keep up the great work!

[@BryanJenks]

You're so welcome! Im glad it's helpful :)

[@Quetiapiness]

Man you really broaden my horizon! One of the best tutorials I've ever found on how to use Zotero and Obsidian together. ~

[@BryanJenks]

Awesome! I'm Glad you found it so helpful! :)

[@ok9gamer65]

OMG. This was insane. I never took notes inschool and college and have always regretted it, note taking is not my thing only, now I am starting my PhD journey and was looking for something like obsedian, found obsidian and cried for a month cz could not do anything with it....watched 25 hrs of youtube videos on obsidian but atlast found this and it changed my life bro............. thanks so much.. so so much. watched this 16 mins video for two hours...hahahaha

[@BryanJenks]

Glad the video helped! :D

[@KevinMullet]

I've been using and promoting Zotero for years, I'm only nine minutes into the video and ALREADY I'm learning stuff I didn't know. What a kick!

[@BryanJenks]

always more to learn!

[@polystyrene_gangster]

In zotero 6 the "extract annotations" function of zotfile has been replaced by a native zotero function called "add note from annotation"

[@joaobraz7575]

Apparently, Mdnotes plugin does not work properly with Zotero native annotation to plain text converter. I had to downgrade to Zotero 5 to make it work. Do you confirm this, Jenks?

[@BryanJenks]

yeah, zotero 6 wrecks the workflow

[@otavioalves813]

@@joaobraz7575 Como você fez o downgrade para o Zotero 5? Onde baixa?

[@sergidela94]

Thank you! I am struggling installing plugins in the newest version (Zotero 7). How sould I proceed? Thank you

[@BryanJenks]

Not really easy to help you through KZbin comments

[@remerose1140]

Same issue

[@OwenVachell]

INSANE! You’ve just changed my life. Can’t thank you enough.

[@BryanJenks]

🙌

[@OwenVachell]

@@BryanJenks do you know a good iPad app that will integrate well with this workflow? My annotation weapon of choice is. my iPad. I've tried PDF viewer, PDF Expert, the native Apple Preview app, Apple Books, GoodReader. None of them seem to save my annotations to the original file, and therefore with Zotero (NB: The PDF in question is a linked file in Zotero, not a copy of)

[@BryanJenks]

@@OwenVachell yep i have the ipad and zotero workflow video planned very shortly and it will work off of the same files not duplicates

[@OwenVachell]

@@BryanJenks awesome! Can’t come soon enough. Thanks so much for the awesome advice on this channel.

[@BryanJenks]

@@OwenVachell glad you find it helpfl!

[@chrisso1973]

Outstanding tutorial Bryan, this is just what I’ve been looking for. Thank you! Please do more on your Zotero - Obsidian workflow. These apps compliment each other so well and I love that they’re free and community driven. 👍🏼👍🏼👍🏼

[@BryanJenks]

Thanks, will do! Really looking forward to the beta working out the kinks or the plugins catching up so the exports from the Beta's PDF annotator supports the Zotero URI links

[@stephenduff1917]

@@BryanJenks out of interest, what parts of this work from Endnote?

[@ElRealista.]

You know if you copy and paste the note from zotero it copies the hyperlink as well? You don’t necessarily need MD notes plug-in. This is useful if you don’t want to copy all highlights but only those you are selecting for your bibliographic note for more atomic and conscious notes.

[@BryanJenks]

👀

[@TharinduWeerasooriya]

I know this is old, but did you consider automating the process of Zotero to Obsidian? Even filling out the basic author details.

[@BryanJenks]

i set it up not too long ago, when i get back to reading and annotating more papers i'll likely make it even more robust and make a video about it

[@christophhaug]

Thanks for explaining this! One thing I wonder: what you showed was *first* reading and annotating one paper and *then* use it in obsidian for further processing. What happens if I go back to the paper in zotero and add some more annotations which I then also want to use in obsidian? I suspect that there is no way in zotero to export only those notes that havn't previously been exported, right? So I would have to export all of them again. If I then import the new export into obsidion I will have duplicates. Not that it's necessarily a big deal to have duplicates, but it becomes even trickier when you work with multiple papers. My ideal would be to have all my zotero annotations (from all papers) accessible in obsidian. So I can I do one big export for and import into obsidian, right? But now assume that you take some new notes in Zoterao. Either on an new paper or on a previously annotatde one. In order not to lose track of those changes in Obsidian, I would have to re-import the relevant annotations pretty soon. And that's not exatly the kind of stuff I want to be doing. Long story short: do you have any ideas for a more automated way of syncing between the two programs?

[@BryanJenks]

a very simple idea would be to have your exported annotations in the markdown file added to your vault remain untouched. if you update your Zotero annotations and export them again then the file contents of the original notes can be overridden and always updated. but for the notes/further processing, you perform on those extracted annotations, in THOSE precipitate notes, if you reference the name of the literature note with a link then the files will always remain linked and you can find all the notes you yourself took on the exported content even if the exported file is completely overridden and updated. This way you can easy keep things current but also retain the linkage to your existing notes and create more over time. Good question.

[@christophhaug]

This sounds great! "Don't touch the exported files!" makes perfect sense! Now I just need to find a way of automating/scripting the export. Should be possible, even when you're on Windows with no Alfred to assist ypu...

[@youtube_research]

Bryan thanks for all the work you put in to make this video. I made it to the point where you copy and paste the markdown script to an obsidian page. I am able to paste the plain text, but could not get the link which will direct me to that particular page in a PDF where I made the note (which I think is the crux of what made this video stand out among other great things you covered here). I have Zotfile and MD notes on Zotero, and has just now plugged in "Citation" and "Zotero Integration" on Obsedian. To add, I am on Zotero 6. I can see that Zotero could have caused an uproar to the workflow, but I was not sure as to whether my problem had to do with the version update or it was just me that who could not figure out how to properly set up on Obsedian (This is my Day 1 on Obsedian). If you could help, I would highly appreciate it. Many thanks in advance. + So, what I differed from you were 16:16 I did not have a template to put it up as you did 16:35 I did not have a text edit key on my Obsedian set up 16:52 I do not have links that will lead to the PDFs (and therefore notes in them) 17:20 I want to open it like this but I still have not figured out how to do so I really wonder what is causing the problem. Wondering whether it has to do with what I do with Obsidian or Zotero.

[@BryanJenks]

updated zotero workflow video coming soon, Zotero 6 broke the workflow with Zotfile

[@youtube_research]

@@BryanJenks Awesome. I will be waiting for it.

[@tom22333]

@@BryanJenks is this out yet?

[@mariokhan20]

Hey Bryan, Thanks for this video as someone new to Zetro and obsidian. It helped me a lot to efficiently use it for my research. More power to you!.

[@BryanJenks]

Glad you enjoyed it!

[@dankort]

Very nice, thank you. Is there an easy way to automatically update the annotations?

[@BryanJenks]

Not that I know of

[@dankort]

@@BryanJenks Thanks for your swift reply

[@PaulFWatts]

Another great video Bryan! Very helpful and practical content. Also greatly appreciate you include a timeline with you video. I just copy the video link and timeline into Obsidian in markdown format and I can then I can just click on a time stamp link to revise any segment whenever I like.

[@BryanJenks]

My pleasure! makes it easy to not waste others time :)

[@meta5175]

Thanks for the great tip! Now I don't have to type everything in my notes! I'm at 2023 and zotero actually offers the pdf reader and note export natively so no need for the plug ins, but I wonder how did you get those quotation blocks 16:41? Is that some theme or custom CSS or something? Mine after importing are in quotation marks and not in > quote blocks, and they're indistinguishable from the notes I made.

[@BryanJenks]

new up to date video on all of this is coming very soon, this video is outdated

[@pianoman723]

Hey @Bryan, thanks for explaining this workflow! Wondering if you've found a way to export little screenshots or selected images from papers? I'm constantly needed to refer to a map or a chart, things that don't translate well (or at all) in plain text. It would be amazing to have an annotation in this workflow that grabs an image from the document.

[@BryanJenks]

Responded in discord :)

[@boxnkola]

Seems you can now do all this without any addons, just select "Add Note from Annotations" which will export the highlights and notes. You can then export this by right-clicking on the new folder that appeared and select "Export Note". Make sure markdown is selected, and choose whether you want the Zotero links or not. Then you can just copy and paste the contents of the resultant file into obsidian.

[@BryanJenks]

i dont like to click that much xD

[@malongfan7772]

Hey could someone tell me if this is working right now? Cause Zotfile doesn´t show me the options, that Bryan had in the video, like to extract the annotations.

[@BryanJenks]

Zotero 6 release broke the workflow, video update coming

[@TheJoshtheboss]

Thanks for the video. Quick question.. What is the benefit of moving notes to Obsidian. Zotero (albeit primarily a reference manager and not a note-taking software) has excellent note searchability, relating function and tagging ability. I haven't used Obsidian yet, but doesn't Zotero provide similar cataloging, aside from the Graph view? Thanks.

[@BryanJenks]

bidirectional linking and unlinked mentions plus more powerful query tooling is available. its no contest, obsidian dominates

[@TheJoshtheboss]

@@BryanJenks Thanks.

[@itfrom]

Incredible! Really helpful. Thank you.

[@BryanJenks]

My pleasure!

[@theawesomesandbox]

Omg, this channel is the find of the week

[@BryanJenks]

glad you think so!

[@rositamantilla2093]

Hi Brian! I followed your advice a while ago and it's great! However, now that Obsidian released the properties my literature notes template is not working. Do you know how to fix it? I'm trying to see if you have another video about this. Thank you!!

[@BryanJenks]

What about it is not working? The properties just take over for YAML so the templates shouldn’t really be affected

[@rositamantilla2093]

@@BryanJenks I'm not sure how to describe it exactly. Basically, the property has an interrogation sign in both the template and in every new note that I open and I insert the literature note template. Does it make sense?

[@PedroMendonza]

Thank you, Bryan. This video is just AMAZING. You have no idea how much this helped me.

[@BryanJenks]

You're very welcome! Im so glad it's helped :)

[@jimboles7474]

It looks to me at 5:09 you are in zotero's desktop version because the File, Edit, View, etc menu items are showing. These menu items DO NOT show in the web version of zotero. RR support informed me that RR does not connect to the desktop. What's going on here?

[@BryanJenks]

RR connects to the zotero sync library i think?

[@LoupSauvage]

This is very helpful Bryan. This is a lifesaver for new users like me. Anyway, how do you put direct quotation to box like in 18:06?

[@BryanJenks]

the quote syntax in markdown "> this is a quote"

[@LoupSauvage]

@@BryanJenks Thank you Bryan. It seems that the updated version of Zotero doesn't work like your tutorial anymore, as it doesn't export the md with the > character before any quote. Thank you anyway.

[@eyeojo]

Thanks! Really helpful as I am just getting started with Obsidian and Zotero

[@BryanJenks]

hope it was helpful!

[@stockholmsyndromeself-trea7517]

This is great! Thanks a gazillion Bryan.

[@BryanJenks]

You are most welcome!

[@danielestevez-barcia2737]

Hi Bryan, I was struggling with research literature management and this is just what I need. There is only one caveat though as of now mdnotes is not compatible with the newest zotero version. Do you know anything about this, are they working on it? Is there any workaround? Thank you, always nice to see your workflows.

[@violetalondono3205]

Hello!! look here, there is the solution forums.zotero.org/discussion/comment/405736#Comment_405736

[@BryanJenks]

new video coming soon!

[@rakeshpatibanda796]

Hi there! I am not getting the links to the PDF when I export the annotations.

[@BryanJenks]

Zotero 6 no longer produces them with zotfile, see the more recent zotero videos

[@theochry6984]

Hello dear Bryan! Thanks for the great work! I'm new to obsidian. Do we need your template in order to have clickable links? I followed the steps and when I entered the md data in obsidian there are no links in there. Thank you :)

[@theochry6984]

It's ok I found it. I had to choose "export note" on the Annotations files and choose "Include zotero links". It works perfectly!

[@BryanJenks]

glad you found your solution :)

[@nutube6291]

Installed Zotfile (as per your instruction). However, I am not getting "extract annotation" option under "manage attachmments." [I have only two options: 1) rename and move 2) get table of contents]. Help!

[@BryanJenks]

zotero 6 threw a big wrench into this workflow >.>

[@nutube6291]

@@BryanJenks Yes, I've found that out recently. Thanks for the reply.

[@seol1500]

@@BryanJenks Can you share your latest workflow with zotero please?

[@kl2920]

Thanks for the video! I have an issue with Extracting the annotations. I get an error that says, "Attachments skipped because they are top-level items, snapshots, or the file does not exist." What could the issue be?

[@GabrielRodrigues-qw1qq]

Right click -> Create parent item :D

[@kl2920]

@@GabrielRodrigues-qw1qq Thanks so much! It worked :D

[@BryanJenks]

interesting that everyone seems to be encountering this issue, i've never had it occur for me.. but glad you all found a solution for others to use to!

[@chinoquant]

Any chance you can show something about the Zotero OCR plugin and how it works? Or if you have another way of OCR'ing a PDF that retains the image of a scanned book, that would be great! Or any other suggestions you would have on going about that process. Lastly, if you haven't seen the Better BibTex plugin for Zotero, that looks quite useful. Thanks!

[@BryanJenks]

never used the OCR plugin. got a link? i use better BibTex!

[@chinoquant]

@@BryanJenks github.com/UB-Mannheim/zotero-ocr this link is from the zotero plugin page. I haven't tried because it looks a little complex to set up...

[@davethinkingsystems]

Really nice. The interface on a PC looks a little different to this but there was enough information in the video for me to work it out so thanks for sharing.

[@BryanJenks]

im glad!

[@davethinkingsystems]

@@BryanJenks in case anyone else is interested, on the PC when I try and create a notes file, I right click on "Container" (or whatever its called) and I get an option "Add note from annotation" in the top level context menu, I don't have to go down into the lower level menu which you have to on the Mac. I click on this and a note appears. I then right click on the note and I get an option "export note", I click on this and it gives me the option to export to markdown. This option allows me to create a markdown file which I can then just copy the contents of into obsidian :-) Very good. I really like this because it means I can ark up pdf books with notes and drop the notes into obsidian and then refer back to the place relevant to the note. Cheers for this. I have to say this video and your big 21 workflow one has changed the way I interact with my computer while studying. Really grateful mate, thanks

[@anniechoi7384]

hi bryan! i'm learning about obsidian and your channel has been incredibly helpful so far. do you have a workflow for extracting kindle notes + highlights into zotero and obsidian?

[@BryanJenks]

i just got a kindle myself so ill be working on that front sometime soon :)

[@arroyocatpumacita2458]

Outstanding. Super useful info for research and learning.

[@BryanJenks]

Glad it was helpful!

[@maximartinezluengo8089]

THIS IS AWESOME!! THANKS BRYAN

[@BryanJenks]

Glad you like it!

[@nehrert]

Grat video. However I do not do markdowns in PDFs in Zotero. I do use Zotero for referens work in my own papers. I would lik to export my litterature to Obsidian. Do you have a video on that?

[@BryanJenks]

thats what this video was about

[@nehrert]

@@BryanJenks Hmm I’d better take another look then:)

[@nehrert]

Nope, didn't find it. Moving on. I did enjoy the zothero thing. And I did not know that Alfred cid all that :O

[@vitokonte]

I was using Zotero for so long and then switched to Papers because I could not insert links in other apps. This combination is so good! Wish I knew it earlier........,.,.....

[@BryanJenks]

sorry it came so late!

[@vitokonte]

@@BryanJenks I am switching to this setup now haha!

[@shenry25]

Hi, really useful tutorial. Many thanks! Background: When I highlight text, many times I only highlight sentences or parts of sentences which read together make up an idea (ie., I don't highlight the fluff). When this is exported, each sentence (or part) is a quotation, which usually doesn't make sense on its own. Also, I prefer it to read as a single summary text, not a bunch of quotations. Therefore, I edit the export text in Obsidian. However, it is really laborious to delete each redundant link, quotation mark etc. Question: is there any way to streamline this tidying up? Not the actual text composition, but removing all the links, etc. Thanks again.

[@BryanJenks]

There is definitely a way to modify the output of the MDNotes markdown extraction, i personally havent done it because i like the format, but there's more details in the forum post about the workflow here: forum.obsidian.md/t/zotero-best-practices/164/57 :)

[@shenry25]

@@BryanJenks it is all question of asking the eight people! 😊Thanks very much that link is helpful.

[@ziweiwang9336]

How do you edit the pdf in zotero in the first place? When I click on the file it opens through other software and does not let me to add notes and does not save to the original file either? As for the notes, I can only add notes separately.

[@BryanJenks]

the pdf's never open "in zotero" its always in what ever pdf reader you have and I'm using preview on macOS

[@anthonysnell4832]

Great video! Do you know how to create citations within Obsidian that are linked to Zotero, and perhaps even a bibliography generator, similar to the integration of Zotero and Word? That would be very useful when constructing essays and articles.

[@BryanJenks]

The exported content from the workflow will give you links back to the documents, but for bibliography generation, i just use Zotero, and you could also take advantage of the zot-hero alfred workflow. a hacky idea would be to just use a markdown link with your citation text and a Zotero URL this worked for tidy data in my vault: [Wickham, Hadley. “Tidy Data.” Journal of Statistical Software 59, no. 10 (August 2014). doi.org/10.18637/jss.v059.i10.](zotero://open-pdf/library/items/28GS4KL8) it's a little extra work to set up, but if done as you got and not doing a giant export it may be more feasible

[@polinafebruary]

Thanks for the tutorial @BryanJenksTech! Does it mean that annotations export is possible only when PDFs are stored in Zotero (not just linked to an external directory with PDFs)? The reason why I am asking this is I don't have the Export Annotations option in my Zotero (Zotfile installed).

[@polinafebruary]

Solved: in Zotero 6, Zotero introduced default option to extract annotations (without ZotFile)

[@BryanJenks]

you got it :) no zotfile! check out my latest video on the topic

[@JuGGerJuGGs]

For me, it doesn't format the '>' character for the quotes. Is there something you did to get that?

[@BryanJenks]

i dont think i did anything special for that... the workflow shouldnt even work anymore due to the zotero 6 update

[@JuGGerJuGGs]

@@BryanJenks yeah, I discovered that not long after posting the comment. As of now, when you create a note from annotations, it'll autopopulate a title called "Annotations (date)" which I'd love to learn how to make into author-annotations automatically. I've been playing around in the config file on the advanced tab of Zotero preferences and I know which parameter to change but I can't seem to append the first author's last name to that title. What I did learn though, is that you can auto back quote your annotations by editing one of those parameters with . Now I'm just trying to change the automatically named title of my annotations. I even set up a script that checks my downloads folder for .md files every 5 minutes and auto moves them into my inbox folder for obsidian for me to deal with. This way all I have to do is download my annotations and continue researching instead of disrupting my workflow trying to finish the note. The problem with that was I kept seeing a flicker on my screen every 5 minutes (I'm not an experienced coder, so I just deleted the script and now I just run the command manually after I'm done collecting information and I want to import them.

[@madelineschiappa1299]

I have followed this tutorial but for some reason the annotation links to the file are not present when copying the exported mardown file. Do I need additional plugins other than mdnotes and Zotfile you discuss? Is this due to recent updates? Thanks!

[@madelineschiappa1299]

Update: there is a package that is still compatable called MarkDB-Connect, this fixed my issue!

[@BryanJenks]

zotero 6 threw a big wrench into this workflow >.>

[@bexturner1]

Hi Bryan, Thanks for this - extremely helpful. I have come across a small issue I wondered if you had any work-round on. I use Zotfile to save my PDFs on OneDrive (rather than within Zotero) to save space as I have already run out of the free storage space (and currently can't find a way to use Mendeley in this workflow!). This breaks down the linking component of your workflow. Therefore, I instead inserted a link to the PDF on OneDrive online, but I cannot specify a page number and so I have lost the ability to jump to particular sections in documents. Do you know whether this function will only work for files stored in Zotero or is there a way to link to passages in PDFs stored in other clouds? Thanks in advance :).

[@BryanJenks]

Thank you for the well phrased and context aware question, this made it easy to answer :) i just tried to add the little piece of the url that allows the page jump to the end of a one-drive hosted pdf and it's a no-go. Doesn't look like that functionality exists at first glance. Sorry!

[@bexturner1]

No probs, thanks for having a look!

[@dr.braddavis1710]

I have been using Zotero for a while but now for some reason when i try to open a PDF it always says it is an unsupported format. It opens in PDF expert but when I change the default to Zotero it's a no-go. Any advice ?

[@BryanJenks]

the pdf should be opening in a pdf viewer program, Zotero is not a pdf viewer program, it is a reference manager that holds your files, its hard to debug this way but i it sounds like you're trying to open the pdf to be viewed in Zotero, this is not possible, it is not like Mendeley in that respect, the pdf's will open in a pdf viewing program like Preview, Acrobat, Sumatra, Zathura, etc. hope this helps :)

[@jingnie1636]

Just updated Zotero 6 but the add-on mdnotes is not compatible with it, any suggestions? Thank you!!!

[@BryanJenks]

revert until it is, it just still isnt compatible

[@mzwlevi]

Hi, Bryan. I am very interested in your Mdnotes template, but I don't know how to set it. It looks like different from Obsidian templates. Could you share the Mdnotes template? Thank you! 🙏

[@BryanJenks]

i only just set them up the other day and never shown them on video before, so you're seeing the defaults actually that or you're talking about my normal templates i use in which case you can get a copy of them by signing up to my newsletter :)

[@manika1897]

Loved the video! tks a lot! Im just having trouble with the pdf editing, when do you open it, does it happen in the own Zotero program?

[@BryanJenks]

depends on if you're using the beta or prior version

[@kvviswana]

Phenomenal workflow, very well explained. Excellent job!

[@BryanJenks]

Thank you :)

[@zabouti]

I tried following your example to extract annotations, but got this error message: Zotfile: Extracting Annotations... Attachments skipped because they are top-level items, snapshots or the file does not exist. Can you tell me what it means? Thanks. I'm determined to learn your system. - ge, chapel hill, nc

[@BryanJenks]

so you're probably extracting the parent item that if you open the dropdown you see the pdf under it, you're extracting annotations from the PDF not the parent item so select the PDF doc and then extract

[@zabouti]

@@BryanJenks I got it to work finally on a different PDF. I'm not sure what went wrong with the first one, but I'm optimistic now. Thanks for your help!

[@chrisso1973]

Pow! Life=Changed. Cheers Bryan, this is ace.

[@BryanJenks]

:)

[@sharfarozsatani4382]

Thank you so much! This solved a huge problem for me.

[@BryanJenks]

You're welcome! Glad to hear it was so helpful!

[@ventana100]

Hi, this is a great video, I really appreciate it. Do you know what might be the reason I can't see the menu you see when trying to export a Zotero note to markdown? It looks like I didn't installed md notes, but I did. Thanks again!

[@BryanJenks]

Did you also install zotfile?

[@ventana100]

@@BryanJenks Yes, I did and it works with no problems :-/

[@mikethelma]

Hi Bryan, I'm working through your workflow and I hit a snag right off. Here are my steps: - Selected a web page in my browser - Printed it to a PDF - Dragged the PDF into Zotero folder - Double clicked it and it opened in Foxit reader - Highlighted text and added a note - Closed and saved the Foxit File - (Double clicked in Zotero to be sure that it would open my annotated file. It did.) - Selected "extract annotations - MESSAGE BOX in lower right. Zotfile: extracting annotations. ERROR: "Attachments skipped because they are top-level items, snapshots, or the file does not exist." I'm guessing that there is some problem creating a PDF by printing to a PDF? Is there a better way to capture a web page? I saw you using a plugin to get a PDF file living on a web page. I did not see what attachment that was ... and, in any case, what I'm trying to do is get the web page itself from the website. Do you have any thoughts to share that might help me move on past this glitch? Thanks for any help you might be able to provide.

[@BryanJenks]

this type of debugging is better done here: github.com/BryanJenksCommunity/FAQ/discussions

[@kaylagreenstien9069]

I have zotfile but when I right click and go to manage attachments it only gives me the option to 'rename and move' or 'get table of contents' --- any thoughts on how to fix this??

[@BryanJenks]

i have a new zotero video coming VERY soon that updates my workflow with the new system

[@kaylagreenstien9069]

@@BryanJenks Excellent thanks so much

[@kamalaakarsh]

Nice video Bryan. One question. I am not into academic research or anything like that. Is there any tool that does similar work as Zotero, but for general PDFs? Like if I can just highlight PDF docs and then export it as markdown. Is there any tool that you recommend?

[@BryanJenks]

i havent used any other method to markup and extract annotations from PDF's other than this workflow. But you dont need to be an academic touse Zotero so the workflow could work just the same for you :)

[@expeditioner9322]

I have a trivial query. Which tool are you using to highlight and annotate PDFs. Is it a Mac only tool?

[@BryanJenks]

i responded on your other comment but its the default MacOS pdf viewer called 'Preview'

[@rexhunter8236]

Nice content man! You gave me some inspirations on how to set up my workflow. Anyway, are you planning to upload a video talking about your Obsidian to Anki workflow? I’m really curious to see how your workflow is set up and how your Anki looks like. Cheers mate!

[@BryanJenks]

Im glad my content has been helpful! I actually haven't gotten into the habbit of using the Obsidian to Anki script/workflow because i actually enjoy anki by itself and dont put non-curated material into my vault, meaning im not taking notes like in a class and then picking what material to remember and then putting that material into the document to be pulled by the script. i manage anki separately. Though the video would be a good topic. I'll add it to my queue. i got a lot ahead of it though but it will come eventually :)

[@maya6090]

I do not have the option to extract annotations when I right click on the PDF. When I go to 'Manage Attatchment' I only have the options of 'Rename and Move' & 'Get Table of Contents'.. I have Zotfile installed. Not sure if it's a Windows issue or something has changed with Zotero/Zotfile. Anyone else had an issue with this?

[@BryanJenks]

zotero 6 threw a big wrench into this workflow >.>

[@stefanleonard4686]

Hi. I tried to install zotero mdnotes but it warns me like this: "The add-on "Mdnotes for Zotero" could not be installed. It may be incompatible with this version of Zotero." What should I do?

[@BryanJenks]

use the older version of zotero until the new one supports mdnotes

[@aleargo8137]

Thank you very much Bryan, it's awesome! I have only a doubt: what if have i to switch PC? The Zotero's links go doesn't work anymore, right? Is there a solution? Thank you very much

[@BryanJenks]

the URI links should work regardless of system

[@aleargo8137]

@@BryanJenks thank you very much

[@estel27]

this was verrry helpful thank you!

[@BryanJenks]

My pleasure!

[@MrCromakey]

Amazing! So good! Thank you!!!

[@BryanJenks]

Glad you like it!

[@neeluvikas]

i tried everything to the T but when i paste in obsidian there are o links back to zoroto documents

[@BryanJenks]

This video is out of date, next Monday latest updated video is dropping on the workflow ✅

[@ovidiubunea3821]

I don't have the option to export the zotero note to markdown (15.17) Any idea?

[@BryanJenks]

Do you have both the zotfile, and mdnotes plugins installed? are the pdf's actually inside the zotero database and not just loose in your file system? if none of these fixed it, consider contributing to this issue so we can help others with the answers we find: github.com/BryanJenksCommunity/FAQ/issues/11

[@ovidiubunea3821]

@@BryanJenks Great, thank you! I did not have mdnotes installed. Now is ok!

[@BryanJenks]

@@ovidiubunea3821 awesome!

[@luiscardoso6578]

Excellent video!!! Really helpful!!! I have question related also do article’s citations (more in the sense of bibliometrics)... Let's suppose you’re conducting a SLR (Systematic Literature Review), and there you are building your bibliographic database: collecting, analyzing (bibliometrics) and reviewing key articles related to your research theme (question). Especially for the second step (bibliometric analysis), it’s very important to have, for every single article you collect, well identified and organized bibliometric information such as: 1) bibliographic citations (number of citations, but also the identification - DOI/ author's name - of all other articles which have cited each article composing your bibliographic database); 2) bibliographic references (number of references but also the identification - DOI/ author's name - of all other articles which have been cited by each and every article within your database). This will allow you to perform (using other softwares) a bunch of interesting analysis, for instance: “CNA” (Citation Network Analysis), among others. Does Zotero also organize/ store such kind of information (bibliometrics) for to each single article of a created collection? If so… Does it do it automatically or does it need to be input/ organized manually? If not... Is there a "Plug-in" capable of adding such functionality to Zotero?

[@BryanJenks]

Lol got at you on linkedin

[@Liz-gc6gn]

🎉 So so awesome!! I’m going to do this. Thank you.

[@BryanJenks]

🥰

[@russbarker9869]

Hi Bryan, Thank you for making this video. I've been playing with using obsidian with zotero this weekend. I'm having trouble getting the extracted annotations to link to the specific page in the pdf. I've gone through the zotero forums and changed some options...nothing seems to be working. Whenever I click on the annotation link, the pdf always opens to first page. I've tried both Preview and Adobe. I'm on a Mac. I think I'm missing something simple...?

[@BryanJenks]

for annotations are you making the notes by right clicking the highlights and adding a note to them? honestly i dont know whats going wrong, could always try reinstalling the addon and trying again

[@russbarker9869]

@@BryanJenks I'm highlighting and making notes in the pdf article. I tried reinstalling, but it didn't help. It's not a huge deal. Just bugs me that I can't figure out the issue. I appreciate your time and assistance.

[@Sebastian1998844]

Amazing video! I have one problem tho. I've been trying to use Zotero's built-in PDF viewer as you do in this video. I haven't been able to do it even though I've downloaded the Beta versions and installed the necessary plug-ins. Do you have any suggestions in this regard?

[@BryanJenks]

i think you're the one who said they figured it out in my discord, yes? :D

[@Sebastian1998844]

@@BryanJenks yup haha sorry about that.

[@AlpineAddict]

@@Sebastian1998844 What was your solution to this? I can't seem to extract annotations that were done in Zotero's built-in pdf viewer.

[@Sebastian1998844]

@@AlpineAddict I stopped using it cuz the beta version didn't work properly anymore (I know it's beta but still). I wasn't able to import my annotations after the last update so I did a backup and installed the regular version. I'm using pdf viewer until they release Zotero 6. I've heard it'll be soon tho. Sorry I wasn't able to help you a little more.

[@AlpineAddict]

@@Sebastian1998844 Ah no worries thanks. I've just disabled the built-in viewer and will use an external pdf program for now. I can't wait for Zotero to finally release the full versions of the desktop and iOS apps!

[@ac8616]

You are a lifesaver! Thank you so much for this helpful video.

[@BryanJenks]

Glad it helped!

[@lizafakirova6285]

Hi Bryan! It's a great tool! However in my case after transferring mdnotes file into Obsidian the link does not go to the specific page in pdf where the note was taken. It always goes to the fist page of pdf. Do you know what can be the reason and how is it possible to solve? Thank u in advance:)

[@BryanJenks]

hard to troubleshoot via youtube comments (im obviously behind on answering them too) try asking here: github.com/BryanJenksCommunity/FAQ/discussions if its still an issue

[@EranKatz]

Thanks Bryan! This is really helpful. Do you have any idea if I can implement a similar workflow with Mendeley? I've been building my research paper library on it for years and I'd rather avoid the need to move to Zotero which seems daunting (not the software, the move)

[@BryanJenks]

Not that I know of, mendeley's annotation export feature was the one that made me run from it to begin with because it wasnt portable data (plain text) they're also not opensource and therefore not as extensible as Zotero.

[@EranKatz]

@@BryanJenks thanks. I need to do some thinking :)

[@BryanJenks]

@@EranKatz i'll try and take a look at mendeley sometime this weekend to see if I can find anything out for you, the ADHD brain will likely forget, so if you'd like to hit me up either via email/discord that's the best way to remind me to do that for ya and get back to you with what I find :)

[@GustavoMontanha]

let's say you export the annotations and put them in an obsidian note. what happens when you change the annotations on the pdf using zotero - do they get updated on you obsidian note or you have to do the whole process again, that is, it's a static process, it does not update the new annotations... is it so?

[@BryanJenks]

its a one way operation. they're not linked at all as the annotations are extracted to a plain text format

[@Registra_AI]

How can I get the notes from zotero 6 in obesidian? Is there any plugin?

[@BryanJenks]

video coming soon!

[@adityapradhan7201]

Can you please mention which css are you referencing here? Also with the latest zot and md note versions. I am unable to open the links from obsidian. Is anybody else facing this issue?

[@BryanJenks]

zotero 6 threw a big wrench into this workflow >.>

[@Mufasimba]

Nice video! I have downloaded the "pack" and like this alot. However Preview seems to have trouble saving all that I annotate, it discards approx. 70% of what i annotate, randomly. Frustrating as hell I might add. Does anyone else have this problem and if so, was there a solution?

[@BryanJenks]

I prefer highlights for the pdf reader on mac

[@Mufasimba]

@@BryanJenks I just downloaded it. Also saw that you have a video where you cover (at least parts) Highligts. I´ll give it a go. Thanks!

[@AlessandroCapobianco]

Stunning tutorial. Have you ever thought to use other software to comment .pdf like Liquidtext?

[@BryanJenks]

i havent heard of that one! i'll check it out, what do you like about it?

[@AlessandroCapobianco]

@@BryanJenks The app allows you to manage in a very smooth way the comments. You can even connect comments between different documents.

[@BryanJenks]

@@AlessandroCapobianco thats neat, kinda like a network of annotations between the documents!

[@5708R]

This is really cool, thank you. Also, first time I'm seeing templates and it looks super interesting (will watch your video on them next!). I was wondering though, is there any way to cite papers in Obsidian via Zotero? I'm thinking where/how to process some general notes that I tend to have on a certain paper, in addition to comments on specific parts. I would like to eventually have both comment/highlight notes and those general notes in one place (e.g., connected in Obsidian). Any thoughts?

[@BryanJenks]

theres a plugin for it that uses zotfile ( i think ) to export an updated CSL JSON file so you can live cite papers

[@TheTanvirahsan]

Bryan, I don't understand where I am making the mistake, but my obsidian links are just not working. Obsidian's version is v0.14.6 and my Zotero version is 6.0.8. I am getting the links but when I click them instead of leading me to the corresponding pdf file it's showing me the URL details and leading me nowhere. Can you help me?

[@BryanJenks]

zotero version update has wrecked havoc on this workflow, update video coming

[@Tsomaia]

"Zotero, you know where this is, give it to me! Awesome." Bryan Jenks, 2021.

[@BryanJenks]

LOL

[@sukpoiu]

I followed along with the same Tidy Data PDF, and I ran into a strange issue: When I extract annotations, it deletes any instances of double- letters For example, "A huge amount of effort" (first 5 words) becomes, : "A huge amount of eort" (the double-f's get removed in my extracted annotation) Anyone know how to fix this?

[@BryanJenks]

thats very odd .__.

[@__archive6650]

Couldn't find an option to like the video twice so bought you a coffee 😁 Many thanks for such informative video!

[@BryanJenks]

So nice of you! thank you! :))

[@fvc1612]

Hi Bryan! Great video. I use windows and I’m worried about what happens if I loose my Zotero local files. Will my files still be saved in the Zotero cloud?

[@BryanJenks]

Yes it will

[@IvanferreroIt]

Thank you for the video! Just a question: why don’t you keep everything inside Obsidian? Most parts of your workflow (maybe all of them), may be accomplished inside Obsidian, is it?

[@BryanJenks]

right tool for the right job, i might be ABLE to do everything in obsidian, but other tools might be better suited for my use cases. Just because a kitchen knife can cut anything, doesnt mean i'd use it for surgery :)

[@IvanferreroIt]

@@BryanJenks agreed and brilliantly stated. 😂 Thank you for the reply.

[@timbushell8640]

Always... ... 🐄 Thanks for this - will be slicing this into my work flow - with Z and O via Chrome, nicely done.

[@BryanJenks]

🐄 Awesome! Glad you found some value in this! :)

[@海洋大學詹凱文]

This is fantastic!

[@BryanJenks]

awesome!

[@zapy422]

Anything for someone coming from Mendeley?

[@BryanJenks]

what do you mean?

[@oliverlovelltas]

Omg dude. Thank you so much!

[@BryanJenks]

Glad I could help!

[@alexischerubin7151]

Thank you so much for the video and the explanations, it is very inspiring

[@BryanJenks]

❤

[@campion7038]

Extremely useful. This Boomer is learning a lot from you!

[@BryanJenks]

HAHA I'm glad i can teach you something helpful and useful :)

[@zapy422]

17:49 is amazing.

[@BryanJenks]

glad you think so :)

[@andresorrego6778]

Hey, I just discovered your channel. Thanks for the great content. Did you migrate your vimwiki workflow to obsidian?

[@BryanJenks]

yes! i put my whole vimwiki into obsidian

[@andresorrego6778]

@@BryanJenks I'll give it a try and see your videos. Thanks!

[@BryanJenks]

Welcome to the party :)

[@sabrinapereira7673]

Love this! But trying to set up something similar on windows but can't find a decent annotation tool. Just tried with adobe reader but annotations don't sync to zotero :( If anyone know of a good (preferably open source) pdf reader and annotator please let me know!

[@BryanJenks]

that is a tough one. on windows I've only ever used adobe or sumatra.

[@emmaknightley]

OK, I see what I've been doing wrong this whole time, I never said "knock knock" to my Zotero, I just rudely barge in and demand files. No wonder it hates me! Seriously though thank you for this awesome video!

[@BryanJenks]

Yeah, you need to at least buy Zotero dinner first before you start trying to move files in and out of it. ( ͡° ͜ʖ ͡°) glad you like the video! :)

[@emmaknightley]

@@BryanJenks 😂