Rationale for non-standard PDF annotations?

va1984
If I understand correctly, the new Zotero PDF reader does not perform "standard" PDF annotations -- by which I mean, annotations made in the new reader do not show up in other apps like Preview, Highlights, PDF Expert, Bookends, etc. (I'm not an expert, but over the last few years the developers of those apps have started referring to a "standard" for annotations, and indeed they all seem to be recognized and editable by each other, so I'll assume that there is indeed a "standard" somewhere).

However I also noticed that the new "add notes from PDF" function in Zotero desktop is able to correctly extract annotations that were made with a "standard" PDF app like those mentioned above. This is good, and it points to a situation where those of us who want things to be inter-operable would have to annotate *outside* the official Zotero reader, even if the next step in the workflow is to use Zotero desktop to extract those annotations and add them to the metadata already held in Zotero.

Can someone explain to me what was the rationale behind Zotero's decision to adopt a non-standard PDF annotation system? I'm sure they discussed this somewhere already, so a link may be all that's needed to clarify.

Relatedly: will it be possible to use an "open in other app" feature from the iPad app to be able to annotate a PDF held by Zotero with the standard annotation method? (I don't have access to the iOS beta so can't simply answer the latter question for myself).
  • adamsmith
    edited February 16, 2022
    See the two last bullet points here:
    https://www.zotero.org/support/pdf_reader_preview#additional_info

    which also explain that you don't actually have to annotate outside of Zotero to generate standard (and standard is the right word: they're part of the ISO standard that's PDF) PDF annotations

    I don't believe the iOS app works with other PDF annotators, no. Passing files between apps is not something that works particularly well on iOS, as I understand it.
  • va1984
    edited February 16, 2022
    Thanks for the link.

    The last point you make ("Passing files between apps is not something that works particularly well on iOS, as I understand it.") is no longer true, actually. It used to be the case, but since the last major OS or two, apps on iPad OS can open any file in any location if they want to (eg Highlights lets you open files stored in any "on my iPad" folder, including those managed by other apps, any "iCloud Drive folder", including those managed by other apps, and any other third party cloud service that is compatible with the Files app. Files are opened and saved in the original location. And any app that wants to, can call another up with URL links. So it is actually very easy to ping pong files between apps on iPad now, at least from a user's perspective. I do it all the time.

    As for the explanation provided in the link, personally, I'm not convinced. There are so many apps these days that opt for non-standard solutions in order to offer more features, and add a promise not to lock you in. But whichever way you spin it, having to "export" something in order to have the standard version is not the same as just having the standard version. To name the classic extreme scenario, if Zotero ceases to exist on the same day as an Apple OS update breaks the app, I have a problem on my hands. I lived through the Sente shit-show; I'm still traumatized.
  • dstillman
    edited February 16, 2022
    We couldn't provide this functionality with annotations embedded in the file — it would be unusable. If two people in a group added an annotation at the same time, or even just while the file was left open on one computer, there would be a file conflict. This happened regularly in earlier versions, both in personal and group libraries, and we expect PDF annotation to get far more usage as part of the app. There's a reason other apps that provide annotation syncing work this same way.
    But whichever way you spin it, having to "export" something in order to have the standard version is not the same as just having the standard version.
    If you're happy with the tools provided by regular PDF readers, then you should use a regular PDF reader, not one integrated into Zotero that's trying to provide a new, better experience. You can choose another PDF reader from the General pane of the preferences.

    On the iOS front, see my response here: https://forums.zotero.org/discussion/comment/399083/#Comment_399083
    To name the classic extreme scenario, if Zotero ceases to exist on the same day as an Apple OS update breaks the app, I have a problem on my hands.
    But that's absurd. Zotero is open source, it's cross-platform, old versions are always available, you don't need an account to open the app. There's absolutely no world in which you wouldn't be able to get your files with all annotations out of the app if you wanted to.

    You don't have to use Zotero's PDF reader, nor do you have to use the iOS app. But they work the way they do for very good reasons.
  • va1984
    edited February 16, 2022
    @dstillman
    I know that Zotero doesn't make decide on things like that without good reason, that's why I asked in the first place, so I could understand.

    If I can paraphrase, it boils down to the fact that Zotero chose to prioritize offering good annotation capabilities for groups and shared libraries over sticking to a standard formats, in this particular case. This seems like a really good choice given that I suspect lots of people (esp. in science) seem to work collaboratively in that way. Personally, I may choose to go the standard annotations way, since I really don't see a situation where I need to co-annotate a pdf with others, nor do I use or want shared libraries, but instead I very much value the fact that over a thousand annotated PDFs can be edited seamlessly from a variety of apps. I am relieved to hear that you seem committed to supporting the non-native reader annotation workflow within Zotero for folks like me!
  • dstillman
    Personally, I may choose to go the standard annotations way, since I really don't see a situation where I need to co-annotate a pdf with others
    Note that there'll be some other features you'd miss out on, such as being able to tag annotations and filter for those throughout the Zotero interface. (Currently annotation tags are limited to filtering in the PDF reader sidebar, which makes it possible to add all of a PDF's annotations with a given tag to a note, but they'll be accessible in other parts of Zotero in future versions.) There'll likely be other things like that going forward.

    There are also performance considerations. In addition to slower syncing from having to transfer the file itself after every change, it's harder for Zotero to track changes to external files, so, e.g., if you annotate something externally, there may be a delay before you can search for those annotations in Zotero — you might need to wait for Zotero to notice the file modification or manually trigger reprocessing. But we'll obviously continue trying to support that as efficiently as possible.
  • amysix
    I understand why Zotero annotations won't show up if I open the pdf in something like Acrobat.
    Is there any way to generate and export a copy of a pdf annotated in Zotero that would include the Zotero annotations and could be viewed in Acrobat? Thanks
  • adamsmith
    For individual files, you can use Save As in the File menu while the PDF is open in Zotero. That saves the PDF with Zotero annotations converted to standard Acrobat annotations.

    Zotero also offers you the option to store annotations in PDFs when you export files.
  • amysix
    ah! thanks for explaining that @adamsmith
  • dstillman
    Just linking to our documentation on this, since it was written after this thread:

    https://www.zotero.org/support/kb/annotations_in_database
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