[[Complete Walkthrough]] Zotero & iPad Workflow For Zettelkasten Literature Notes

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  • Опубликовано: 21 ноя 2024

Комментарии • 125

  • @BryanJenks
    @BryanJenks  3 года назад +3

    Want to get your hands on my Obsidian templates, Custom CSS, and Mermaid Diagram code? 👉🏻️bryanjenkstech.ck.page/d4ec0713d5
    0:00:00 What we're talking about today
    0:00:49 Intro
    0:01:00 Getting started
    0:01:17 zotfile.com/
    0:01:28 What hardware / software do i need for this workflow
    0:02:30 Diving into the workflow
    0:03:09 Setting up your Zotfile settings
    0:06:49 Sending a file to the tablet
    0:09:06 bryanjenkstech.ck.page/6bb52f9bef
    0:09:54 Live example of annotating and syncing a document
    0:12:23 Extract the annotations and pull back into Zotero
    0:12:50 Get PDF from tablet
    0:13:46 Extracted Annotations and markup are synced!
    0:14:25 Closing
    0:14:50 How to support the channel and Patron shout out
    0:15:28 Outro

  • @fernandodesouza8276
    @fernandodesouza8276 3 года назад +2

    Working perfectly with Zotero on macbook pro, dropbox and Xodo pdf reader on a samsung tablet. Thanks a lot brother!

  • @maploolake
    @maploolake Год назад +1

    Thank you so much for your detailed instructional video! This helped me a lot with my workflow.

    • @BryanJenks
      @BryanJenks  Год назад +1

      I’m glad you enjoyed it!

  • @martineellis
    @martineellis 2 года назад

    This is so helpful Bryan - thank you. I have just started using Zotero (on year 3 of my masters - wish I had started earlier!) Previously I have been highlighting and annotating PDFs on my iPad using Highlights app which already allows you to extract your highlights and annotations as markdown (which I paste into my lit note in Obsidian). My main database of PDFs was in Notion (very manual process). Now I am using Zotero linked to Obsidian, I think your approach makes more sense as you start by putting the PDF in Zotero - then create literature note in Obsidian that is linked to Zotero - then send PDF to iPad to read. I would still use Highlights to annotate etc (and then send back to Zotero). Your workflow is more logical than what I have been doing. Thank you again for your videos.

    • @BryanJenks
      @BryanJenks  2 года назад

      Im glad you found the content helpful!

  • @ProductivePM
    @ProductivePM 3 года назад +4

    YES !!! Another great Bryan Jenks video! I just really like the workflow. I am setting this up today. Love the ability to use the iPad as the annotator for pdf's. Great job and thanks for sharing. Thanks buddy!

  • @edkako
    @edkako 3 года назад +2

    Super helpful -- I didn't know that Zotfile could be used to enable and extract annotations made on tablets. Very handy!

  • @vickidavis471
    @vickidavis471 3 года назад +4

    Hey Bryan! I watched the live stream of your Zettlekasten work the other evening. Are going to post the video of that? I'd like to re-watch your notetaking of literature notes on scientific journal articles again. I always feel like I write too much and perhaps don't link them in the best way.

    • @BryanJenks
      @BryanJenks  3 года назад +1

      Glad you enjoyed the live stream! My past livestreams are now being unlisted and for patreon/github sponsor supporters only :)

  • @caglarongan
    @caglarongan 2 года назад

    Awesome, thanks Bryan !
    Simply copy-pasting the extracted annotations from the right side panel works just fine for me. Obsidian converts the rich text to markdown automaticly with no problem.
    Only value Mdnotes adds is putting a ">" before the highlights.

  • @asash4101
    @asash4101 7 месяцев назад

    youtube lives on videos like this one. love it! didn't get what the difference btw setting up the whole tablet thing thru zotero and then send the papers to the tablet and having drive synchronization on both devises is. i just started zotero, want to make it efficient using already existing storage (google drive) without buying zotero storage (i am PhD student, i have way too many papers to work with)

    • @BryanJenks
      @BryanJenks  7 месяцев назад

      Glad you liked it :)

  • @drchristiansmith
    @drchristiansmith 3 года назад +1

    Bryan you are an excellent teacher and explaining things in detail. Cant wait for your Obsidian course

    • @BryanJenks
      @BryanJenks  3 года назад

      Oh thank you so much! I'd be nothing without my scripts 😅️ i tend to ramble and tangent a lot (thanks ADHD) but if my style suits you then i am very happy 😊 thank you for the lovely comment!

  • @melaniegeiger6543
    @melaniegeiger6543 7 месяцев назад

    Thank you so much for this video, you made my student life so much easier

  • @ys621
    @ys621 2 года назад

    A cool approach, thanks for sharing. I personally have been splitting the screen on my iPad between Obsidian and a PDF viewer then highlighting and dragging or copypasting quotes above, then adding comments directly in Obsidian. I do have a bigger screened iPad though so maybe I'm a bit spoiled there.

  • @valeriad9236
    @valeriad9236 2 года назад

    Bryan, thanks a lot! Your videos helped me understand the concept that I was trying to build for my study notes! Your explanations are clear and easy-to-use, thank you!

    • @BryanJenks
      @BryanJenks  2 года назад

      im glad you got such value from my content! :)

  • @GavinFreeborn
    @GavinFreeborn 3 года назад +1

    Gotta love it when Linux is supported.

    • @BryanJenks
      @BryanJenks  3 года назад +1

      that webstack though xD

  • @vw9659
    @vw9659 9 месяцев назад

    The Zotfile plugin described here works with the current Zotero v6. But it is not being upgraded for compatibility with Zotero v7, currently in beta. There are alternative plugins that will supply core Zotfile functionality under Zotero v7 (see Zotero Forums for options), but NOT the Send to Tablet function shown here.
    A Zotero mobile app is now available. But it requires that you use Zotero's own online storage (300 mb free) to access your stored PDFs from within that Zotero app.

    • @BryanJenks
      @BryanJenks  7 месяцев назад

      the new workflow im using doesnt use zotfile anymore, please see the newer zotero videos ive made

  • @familiekontoen1955
    @familiekontoen1955 3 года назад +1

    Thanks for the video. I would recommend using Dropbox or another alternative to iCloud that has versioning built in. I have had issues, where my file was overwritten with a non-annotated version on iCloud, with no way of getting the previous version back.

    • @familiekontoen1955
      @familiekontoen1955 3 года назад

      Using Dropbox to access the files on the iPad, you can use the free version of Readdle's Documents app and their PDF Expert app. Both working fine in the free versions.

    • @BryanJenks
      @BryanJenks  3 года назад

      Thanks for the tip!

  • @stephanievanriper8808
    @stephanievanriper8808 3 года назад +1

    Great video, thanks for creating! One question...I have been challenged by the limited/poor functionality of Adobe PDF Reader and Highlights on the ipad...there are better one's out there that I have tried like Goodnotes 5 and Notability...but their functionality does not allow for zotfile to extract annotations (even for just the highlights), which is frustrating. Can you share what other PDF annotators you have tried on the iPad other than the one's listed above that could be options for this workflow and successfully can have annotations extracted by zotfile? Thanks!

    • @BryanJenks
      @BryanJenks  3 года назад

      havent really tried any others. ive used sumatra on windows but not for annotations and what not.

  • @JonWood
    @JonWood 3 года назад

    Interesting video! I've seen some folks using Notability to annotate their PDFs, though, I'm not sure if can extract out the annotations as markdown. Not a bad idea to go through them again input into your vault, though.

    • @BryanJenks
      @BryanJenks  3 года назад +1

      not sure how it looks under the surface but if its a highlight and a note attached to that highlight i've seen many PDF apps all have annotations extracted successfully thus far 🤷🏻‍♂️️

  • @AlexMoophty
    @AlexMoophty 3 года назад

    You are doing a fantastic job! You help me enormously to channel the usual chaos in literature research.
    I have one question: How do you save your PDFs? The Zotero cloud storage is used up pretty quickly. I would prefer to move the documents to my iCloud. However, I have read a lot of negative things online.
    Thanks in advance for your answer!

    • @BryanJenks
      @BryanJenks  3 года назад

      Glad I've been helpful :) this question would probably be better posted here: github.com/BryanJenksCommunity/FAQ/discussions
      :)

  • @chr_aikicom
    @chr_aikicom 3 года назад +1

    Great video, I was just looking for a solution to synchronize highlights and notes made on my ipad with the pdf version in Calibre. Seems it is not possible, so I will try to substitute zotero for calibre

    • @BryanJenks
      @BryanJenks  3 года назад

      Glad it helped!

    • @paullafleur6112
      @paullafleur6112 3 года назад

      Hi Christian, one possible workflow on Mac that I am experimenting with: open PDF from Calibre library with macOS PDF Expert app; apply highlights and make notes; export annotations as Markdown from within PDF Expert app; import the Markdown annotations into Obsidian. This also works on iPad if you put the PDF onto your iCloud drive and use iOS PDF Expert app on iPad. Hope this is of help :)

  • @RobFraser
    @RobFraser 2 года назад

    Thanks for this work around. I was hoping the iOS app for Zotero would fix this. Looks like you can sync the notes and see them on the desktop from iOS. However, cannot currently export a md file from iOS notes due to a sync issue. Hopefully they fix it to avoid this type of work around. Appreciate the video.

  • @forrestrperry
    @forrestrperry 3 года назад +1

    Bryan! Thanks for this. Much appreciated.

  • @aisx
    @aisx 3 года назад

    Tip for android users using onedrive/dropbox/drive: for me trying to access the files via a file explorer would force me to redownload the file in a different local folder. This defeats the purpose if I want to maintain file structure. Xodo pdf and drive pdf viewer both failed in this regard. However, editing the files was not a problem at all using adobe acrobat. Just connect to your cloud service via the adobe acrobat app and then you should be able to open and edit the pdf file from the cloud folder location no problem.

  • @ProductivePM
    @ProductivePM 3 года назад

    Bryan, as a thought, how about a video on using the Query capability just recently announced?

    • @BryanJenks
      @BryanJenks  3 года назад

      i thought i did in the release notes video, but in detail about queries will be in the course for sure

  • @tom22333
    @tom22333 5 месяцев назад

    May be picking up an Ipad. I keep my zotero library of PDFs in google drive. Thinking I might just annotate using a pdf editor from google drive in the files of the Ipad and save them like that. If that works

  • @DavidAAcostaS
    @DavidAAcostaS 3 года назад +1

    Jenks, I have a question: since I have all my PDFs already in Dropbox and they are connected to Zotero as linked files, should I need all the workflow you showed us? Because I guess all the changes I do to the PDFs in my iPad should be updated in Zotero automatically (because they are linked files), so the one thing I should do is extract the notes and highlights with Zotefile... Right? Thanks again for sharing!!!

    • @BryanJenks
      @BryanJenks  3 года назад +1

      if zotero can extract annotations from linked files, then it sounds like you're all set :)

  • @gsatwood
    @gsatwood 3 года назад

    That, is awesome. Thanks for showing how this works.

  • @ShreyasKallingal
    @ShreyasKallingal 3 года назад

    Great video! Kind of unrelated, but have you tried using RemNote instead of Obsidian + Anki? I'm just getting started with Obsidian, but I'm torn between the two. Do you think RemNote provides anything special? I personally like Obsidian because of the whole local storage concept, and portability is a non-issue for me. Thanks for your help!

    • @BryanJenks
      @BryanJenks  3 года назад +1

      Yes I have, briefly. I really like it and what they're doing. Im pretty invested into Obsidian and Anki, but ultimately i think i may do more classroom notes in RemNote and keep my Obsidian vault more for my Zettelkasten. But i just dont have time to learn a new app at the moment. But i may make RemNote videos in the future because i think they're doing some great stuff in a good direction

  • @Kiowafa
    @Kiowafa 3 года назад +3

    Yee-haw! This made me so happy

  • @3self
    @3self 3 года назад +1

    Dude ..... these videos are just A1. lol and mann I been trying to find a way to add MarginNote 3 to my workflow with obsidian, zotero is great but I do a lot of reading on my ipad

    • @BryanJenks
      @BryanJenks  3 года назад

      Glad you like the video!

  • @HegelianBoi
    @HegelianBoi 2 месяца назад

    How do I get the opposite done? i.e. get my annotaitons I did on my pc to appear on my tablet. There seems to be no automatic way of doing this.

  • @bragattemas
    @bragattemas 3 года назад

    ✏ Great job Jenks, thanks for the tutorials.

  • @Quetiapiness
    @Quetiapiness 3 года назад +1

    Hi Bryan. Thanks for sharing. There is this problem with syncing comments of pdf files in the folder of iCloud. How can I edit it and see the updates of the pdf just after closing the pdf file in Adobe? I can not see any changes in the one on iCloud after doing so. Thank you so much if you got time to answer.

    • @BryanJenks
      @BryanJenks  3 года назад

      did you explicitly save the file?
      try just sending the file back to zotero and following the rest of the workflow. sometimes i dont see markup for somereason but after extracting ill have the annotations and then see the markup 🤷🏻‍♂️️

    • @Quetiapiness
      @Quetiapiness 3 года назад

      @@BryanJenks I think my problem was that I imported the pdf file to adobe in my iPad and any annotations I made was saved in adobe but not in the file in iCloud. I watched your video for several times but still failed to find how to do annotations through adobe and save them directly to the file in iCloud.

  • @dr.braddavis1710
    @dr.braddavis1710 3 года назад

    Great video- I have been trying to find a way to add to Zotero from the iPad- Have you found any solutions to that? I tried reversing your workflow and adding right to the folder Zotfile creates from the iPad but that didn't work.

    • @BryanJenks
      @BryanJenks  3 года назад

      im not usually spending a large amount of time on the iPad, but have you tried logging into the webapp zotero has and adding PDF's that way?

  • @timbushell8640
    @timbushell8640 3 года назад

    So - do you batch the return to Z, and or, just the copying into Obsidian, rather constantly back and forth with different documents?

    • @BryanJenks
      @BryanJenks  3 года назад +1

      im not on my iPad a lot but with this workflow now i'll likely be on there more. What it may look like is something like this: drop a paper or papers onto the ipad, read and markup, return to Zotero, extract annotations to Obsidian, complete the rest of my note generation workflow. my ADHD is not conducive to handling lots of different items in different places of different statuses so i try to keep things as simple as possible and follow a rigid taxonomy that i have documented for my own reference and sanity 🙃️

  • @JackBeaudoin
    @JackBeaudoin 3 года назад

    Tall guy, does the workflow in the video produce a literature note in markdown for each extracted annotation on the pdf, or just one markdown file containing all the extracted annotations? Also, what would Sonke say if he saw you highlighting????? ;)

    • @BryanJenks
      @BryanJenks  3 года назад +1

      LOL what i present extacts all items to a single output note, but i just set up some additional zotfile features last night to have each color of annotation highlight extracted to its own file.
      lol i highlight usually because i had a thought or idea from the content and i want a little context for the thought when i flesh it out afterwards, so id venture to guess he'd think it was fine :)

  • @ramysami
    @ramysami 3 года назад

    I just tried Zotero but I didn't like it . I actually use Acrobat on PC and on my mobile and using Adobe Document cloud which is free you can highlight and take notes on either platform an have both sync'd in real time. You can also organize you PDFs in folder and so on.

  • @benbenane7826
    @benbenane7826 3 года назад

    hi, Bryan! thanks a lot ! I am just struggling to understand the workings of the base directory of zotero...How am I able to future-proof cite and backling to the paper? So what of the zotero-settings do i have to backup to achieve that? It would be wrong to change zotero base directory to absolute paths??

    • @BryanJenks
      @BryanJenks  3 года назад +1

      not quite sure what you mean. But if your PDF files are stored within your zotero database and not in your file systems like a folder called "research" on your desktop then no matter where you move the database to, zotero will know what to open when you click the links because of the unique ID in the hyperlinks when you generate them. Thats the beauty of UID's

  • @ColeCoug
    @ColeCoug 2 года назад

    Cool tattoos!

  • @mattiasovesson4447
    @mattiasovesson4447 3 года назад

    Great tutorial! What if I imported my annotations into obsidian but wished to continue annotate the document at a later date, would these new annotations still sync to Zotero? Like if I'm reading a book I might want to import my annotations/notes into obsidian from the 1st chapter and continue annotating chapter 2 at a later date. Does that make sense?

    • @BryanJenks
      @BryanJenks  3 года назад +1

      each time you export annotations in zotero it will create a new annotations file with a date stamp but it will include all annotations from the entire file. There is no live syncing the extracted annotations to my knowledge, unfortunately.

  • @NabhanPhD
    @NabhanPhD 3 года назад

    Cool workflow!

  • @OwenVachell
    @OwenVachell 3 года назад

    Genius! Thanks so much.

  • @jbpines9406
    @jbpines9406 Год назад

    Hello! Is it possible to all do this in iPad for those who don't have MacBooks?

    • @BryanJenks
      @BryanJenks  Год назад +1

      i think as long as you have a computer with an icloud connection like the onedrive folder that lives on a windows computer that it might be possible, but thats just my hypothesis

  • @hayleecs4223
    @hayleecs4223 Год назад

    Big question: how can I see annotations made with Zotero Desktop on my ipad? ZotFile doesn't seem to export annotated attachments...
    eta: currently a workaround is opening the paper zotero desktop, File > Save As... > replace the original attachment file, then send it to tablet. This way annotations will be written to the file before sending it. It would be nice to have ZotFile doing this automatically

    • @BryanJenks
      @BryanJenks  Год назад

      on ipad, just use the zotero app now, zotfile workflow no longer needed as annotation can now be done in the zotero app entirely

    • @hayleecs4223
      @hayleecs4223 Год назад

      @@BryanJenks yep, but I have to buy their cloud storage. I’d like to keep my iCloud/Google Drive

    • @BryanJenks
      @BryanJenks  Год назад

      Their storage was free to a point if I remember, because I haven’t had to pay yet, or are you just at the size limit?

    • @hayleecs4223
      @hayleecs4223 Год назад

      @@BryanJenks 300MB I think, which isn’t much to keep my whole library… it would be a swap memory

    • @matejsmid7927
      @matejsmid7927 Год назад

      @@hayleecs4223 You can create a group library and sync only this, you can set up your own WebDAV share or you can pay 20 bucks for 2 GB / year which I find perfect for such a great service

  • @Trecoolerok
    @Trecoolerok Год назад

    As I can see, this workflow is outdated, because zotero has added pdf reader feature to ipad software.
    What I’m curious about is how to manage files correclty without using their cloud.
    For instance: I have pdf file on my dropbox or mega cloud storage. I add linking to the file on my computer.
    Can I now, having it downloaded on iPad, somehow link this new file copy with zotero on iPad?
    As I am using their sync cloud feature.

    • @Trecoolerok
      @Trecoolerok Год назад

      By the way, what do you think of obsidian highlighter plugin?
      You can use it to make notes on epub files right inside the obsidian. And pdfs too

    • @BryanJenks
      @BryanJenks  Год назад

      i just use their mobile app on my ipad if i wanted to read that way :)

    • @BryanJenks
      @BryanJenks  Год назад

      the output of the plugin is very messy and it just doesnt jive with me, i prefer zotero and extraction at the moment, it seems "cleaner"

    • @Trecoolerok
      @Trecoolerok Год назад

      @@BryanJenks thanks for the answer!

  • @ryanbthiesant2307
    @ryanbthiesant2307 3 года назад

    Can I use the real iBooks folder so I can use iBooks to highlight and make notes?
    Does this duplicate the PDF’s creating multiple versions of the same pdf? For example if cars pdf is in two categories 1 transport and 2 personalisation does this mean two pdfs on my ipad?

    • @BryanJenks
      @BryanJenks  3 года назад +1

      im not sure. ultimately this workflow is treating pdf's held inside zotero as library books you check out and check back in

    • @ryanbthiesant2307
      @ryanbthiesant2307 3 года назад

      @@BryanJenks I guess I need to test this. Thank you. This is a good tutorial.

  • @zedk12s
    @zedk12s 3 года назад

    Thank you thank you thank you

  • @doodah120
    @doodah120 3 года назад

    why does one need to manually get the annotated file from the tablet? Why doesn't it sync automatically?

    • @BryanJenks
      @BryanJenks  3 года назад

      There may be a way to automate that, I just haven't bothered yet.

    • @doodah120
      @doodah120 3 года назад

      @@BryanJenks okay I see, thanks for the reply!

  • @wi-im
    @wi-im Год назад

    Is this working when you have ipad and PC ?

    • @BryanJenks
      @BryanJenks  Год назад

      It might, but I haven’t tested it.

  • @Eisesser01
    @Eisesser01 2 года назад

    But that's way too tedious. Why does Zotero delete it from the synced folder? I would need to re-sync it through Zotero, send it to the tablet, make notes and then retrieve it again.

    • @BryanJenks
      @BryanJenks  2 года назад

      with zotero's new beta, annotating pdf's within zotero combined with their mobile app, theres a lot of good things to come to reduce the hassle of this workflow

  • @DutchArx
    @DutchArx 3 года назад

    This is a way too complicated workflow when you compare it to Papership on the iPad. I would recommend to check that out first.

    • @3self
      @3self 3 года назад +1

      I thought they stop supporting/ updating

    • @BryanJenks
      @BryanJenks  3 года назад

      never heard about this tool, thanks for the recommendation

    • @BryanJenks
      @BryanJenks  3 года назад

      looks like the last release was over a year ago and before that it was 4 years :/

    • @OwenVachell
      @OwenVachell 3 года назад +1

      @@BryanJenks yeah they stopped supporting it. Yet to get the annotation benefits you still have to pay for it.

    • @BryanJenks
      @BryanJenks  3 года назад

      @@OwenVachell yeah i like free 🤣️

  • @SoniaBlanco
    @SoniaBlanco 3 года назад +1

    I love you. Please Marry me hahaha. Just kidding. This is awesome. Thank you

    • @SoniaBlanco
      @SoniaBlanco 3 года назад

      ohhh, but it does not work with groups libraries. Any ideas??

    • @BryanJenks
      @BryanJenks  3 года назад +1

      @@SoniaBlanco never used a group library before so I don't know, their new beta doesn't work with grouped libraries either at the moment

    • @BryanJenks
      @BryanJenks  3 года назад +1

      .___. you're welcome!

    • @SoniaBlanco
      @SoniaBlanco 3 года назад

      @@BryanJenks That's essential for group researchers. I've applied for the beta a few days ago, but still have no answer

  • @bryanjenks3444
    @bryanjenks3444 3 года назад +1

    I haven’t watched the videos of the channel, but I like it already.

  • @YuansterHsu
    @YuansterHsu 2 года назад

    So amazing! It is a cool work