Best PDF tool for annotating & using w/Zotero?

edited November 15, 2024
Hey all,

My head's about to explode I'm getting so many issues with the Preview tool on my Mac, but then also running into seemingly related issues (but maybe not) with Zotero and Google drive. I'll try to lay them out in a basic way here and see if anyone has suggestions / thoughts, etc. (or just empathy cause this is SOOO frustrating)--i'll start w/Zotero since that's the forum i'm on, but it feels like there are good people here who could empathize and offer any suggestions more broadly (I hope!):

1) ZOTERO: I'm trying to transition to Zotero being my central repository for all my academic reading for my PhD. But i'm having this issue where i'll open PDFs by double clicking on them in Zotero; they'll then open in Mac Preview; i'll annotate the hell out of them, eventually close them, saving throughout to make sure i don't lose annotations; then i'll double click on them in Zotero to open them again, and often many of the annotations are just gone! (the Zotero folder they're being saved on is located in the default location on my hard drive as context)

2) GOOGLE DRIVE: I have G. Drive via my school, so i'd like to keep PDFs on there so they don't turn my laptop into a brick w/a glut of files taking up too much room. So i have Google Drive on my desktop, w/my preference set to "Stream files." But if i try to open any PDF that's stored on my desktop G. Drive, and then begin marking it up in Preview, i'll get some errors when i save throughout asking something about overwriting and saving my current version or reverting to the online version. This is infuriating because i similarly will save something in this way (cause there's no other real option i've found), and i'll also open it back up and it won't have all the annotations (not to even mention when i open those PDFs in G. Drive, they often only show underlined annotations, not highlighted!).

3) PREVIEW: It just seems cumbersome sometimes to use, not to mention all the above issues. And i'm trying to figure out a tool i can use in a way i can feel like i'm writing directly on something in that old school way, but on a tablet of some sort w/an "electronic pen," and then make and change edits, updates, etc. on either my laptop OR on a tablet (and so i'd want to be able to access them both). I've heard some about PDF Expert (https://pdfexpert.com/), but it looks like it'd be $40/month at first w/some 50% off, and then probably just go up every year after.

Sorry this is messy and a bit unclear, i'm overrun w/schoolwork and it's all i could do to post something here, b/c this is driving me crazy!!

Thanks for any insights, etc.,

Brendan
  • We can't help with other programs, but you're aware that Zotero has its own PDF reader on macOS and iOS, with support for ink annotations? That's obviously what we'd recommend using.
  • Oh hi, no I wasn't aware of that! How do I access or try that out?

    And sorry what do you mean by "ink annotations"?
  • edited November 15, 2024
    Re 1, PDFs opened from within Zotero should open in the Zotero reader, unless you've changed that in Zotero settings. Most people find that to be the best approach, all things considered. Annotating in an external reader should be robust though, except that those annotations will be locked when viewed in the Zotero reader, unless imported.
    https://www.zotero.org/support/kb/annotations_in_database

    If you occasionally want to open a PDF in another viewer from within Zotero desktop, this plugin makes that easy.
    https://github.com/retorquere/zotero-open-pdf

    Re 2, firstly, we assume you do NOT have your Zotero database on Google Drive.
    https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder

    Secondly, assuming you are using *linked* PDFs stored on Google Drive, the problems sound likely to be associated with have GD set to streaming instead of mirroring. That's probably why GD is asking you to resolve which file you want to keep - the one you just worked on locally, or the original it has stored online. You could experiment with always overwriting, and seeing if that always has the desired result; and stick with streaming if that works. Or you could turn off streaming in favour of mirroring. So that if you make a change locally, it will just be mirrored to the online copy (and vice-versa).

    Re 3, see 1. Also, other people may have recommendations for pen-friendly Mac/tablet PDF viewers (if you want something different to Zotero's), whose annotations are compatible with Zotero's.

  • Ink annotations means drawing, like with an Apple Pencil on an iPad.
  • edited November 15, 2024
    Oh wow, this is great @dstillman -- I am caught up in something so will circle back as i start to work through this, but just wanted to say thanks a million for taking the time, that means a lot!

    All best,

    Brendan
  • Hi again Dan, I'm just starting to experiment with the Zotero PDF annotation tool--i'm very intrigued, this was clearly a massive amount of work you all put into designing this, many thanks for it!

    Is there a best link or other way to learn about what ink annotation tools can be used with Zotero and how?
  • I'm also trying to figure out this question of how to get around storing all these PDF files on my hard drive if I use Zotero's PDF reader for annotations...

    I saw the warnings about cloud storage you noted above, thanks for that.

    It seems like i may need to sift through the "linked file" process and recommendations if i'm going to avoid having all the PDFs on my hard drive--are you able to confirm if i'm understanding that as generally the best way to do avoid storing them on my hard drive (described here: https://www.zotero.org/support/attaching_files#stored_files_and_linked_files)?
  • edited November 16, 2024
    @bhoconnor I guess it depends on your needs really. Zotero's inbuilt annotation works great. One downside might be that it doesn't encode the annotations into the PDF itself. But then this might also be an advantage as its is more efficient to transfer/sync these annotations (e.g. note that even for the beta Android app, the annotation syncs instantaneously - which i imagine is otherwise difficult if one does annotation on the PDF itself).

    On the other hand, if you think that the viewer on zotero does not fit your needs, for example, for some pdfs that i need to study - not just skim - i put them in my boox and do my thing there. The reader is better for stylus support and all the annotations are written into the file. This might be handy, for example, if you want to share this file with your colleagues with the annotation.

    These will have an implication on your workflow/setup. If you use linked files and work across different machines, perhaps you'll need to set up zotero *and* your syncing instances multiple times, which can be daunting.

    It's to do with what you want to do with your annotations. Some people cba with their annotation as they keep a separate document while reading, some do not.

    There's also a wide range of PDF viewers out there. For mac, i guess i could recommend skim. However, alike Zotero, it doesn't natively save annotations into the file. Preview is just laggy with bigger documents. Of course, being a native app on Mac, it has small footprint, efficient, and apple-esque.
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