Annotation app for iPad Pro

I know this has been slightly discussed elsewhere but I am not seeing a clear path for my workflow. I have an iPad Pro (2018) that I want the ability to annotate PDF's that are housed in Zotero database. I was able to effectively does this on an older iPad within the PaperShip app (after paying for the app), but when I did this on the iPad Pro the annotation options are not available. First I tried transferring my paid license to the new iPad but this did not work. Tried paying again, but to no avail.

It seems to me like there would be tons of people out there that would want to do the same thing or am I alone on this? Using the iPad Pro pencil is so nice and the iPad Pro is so much better to read on that a laptop or computer.


And BTW if PaperShip is no longer being sponsored why can you still pay for it? Seems like Apple would terminate payment with no support.
  • Zotero is developing it's own iOS app, but until that is released, using some version of ZotFile's send to tablet and Dropbox (or another sync folder) is probably the easiest solution.
  • any rumors on *when* Zotero might release an iOS app? I've been using Papership successfully, but it hasn't been updated in forever and is getting buggier because of it (occasional crashes). I don't want to switch to another service, but reading and annotating pdfs on my iPad is a big part of my workflow. Zotfile is nice, but you've still got to go back to computer to send stuff over...
  • My workflow: Zotfile Send To and GoodReader to sync that folder (Dropbox, Google Drive, OneDrive, WebDav, etc). Make highlights and annotations and then sync again to the folder and recover from Zotfile.
  • @jesgar if your iPad storage can accommodate your entire zotero pdf archive, you can skip the sending to ipad and getting from ipad steps. Just use zotfile to put all your pdfs in one folder synced on iCloud or dropbox (this can be automated in most cases) and use goodreader to annotate—the annotations will sync automatically.
  • @erazlogo I tried this way in the past but the problem was that the PDFs synced on Dropbox (or any other sync system) sometimes were not right located on another computer (I work on two computers). It was not a problem of selecting the right folder, sometimes a file was not located even though it exist on the right folder and needed to be selected manually in Zotero to regain access.
  • edited November 27, 2019
    I have the same problem after I reinstall Papership (v.3.8.3 (167)) on iPad Air 2: I can use part of the annotation functions by long-press on the screen and select the corresponding annotation tools, but the annotation toolbar disappeared. With iPad Pro(2018), the problem existed from the beginning: no annotation toolbar after the in-app purchase restored to my ID.

    However, the iPhone version Papership worked very well: the annotation toolbar is always there no matter Papership was reinstalled or not.

    So my way around is to use the Papership-app on my iPhone to sync Zotero library and attachments, share pdf-files via AirDrop to iPad, use iPad pro to do the annotation via PDFExpert(GoodReader), share back the pdf-file to iPhone, sync the Zotero library and attachments on Papership again:

    [1]Download the pdf-file in the iPhone-version Papership (you have to first sync attachments from cloud storage, eg. WebDAV server, to the local Papership);
    [2]Go to the annotation toolbar then click 'share'-icon, share the pdf-file to iPad via AirDrop;
    [4]Receive and open the pdf-file using PDFExpert/GoodReader APP on iPad, happy annotating with iPad;
    [5]After editing the pad-file, share back the file via AirDrop to iPhone-version Papership. Select "Update Existing File" on the pop-out options.
    [6]Sync the attachments back to the WebDAV server with the iPhone-version Papership.

    This is really not a good way in terms of workflow. Better to buy a new ThinkPad X1 Yoga (Thinkpad pen included) instead of iPad Pro +Apple pencil.

    Update on 2019-11-27
    The Author of PaperShip update the program to version 3.8.5 and the bug of annotions tool box was fixed.
  • Zotero is currently developing an iPad app, but for now, I recommend using Zotfile on Zotero desktop along with any PDF reader app (Adobe, Apple Books, GoodReader, etc) to annotate pdfs.
  • edited September 16, 2019
    I struggled with this issue as well (former Papership user, the sync kept failing on my regular iPad 2018) and I found the following workflow that suited me:

    Managing the Zotero library works OKish through the web interface / bookmarklet.

    This leaves the sync issue with annotated PDFs: My solution for now is to store my complete Zotero library on iCloud drive. While the folder structure of the library is not easily understandable by humans, it is indexed by Spotlight/Siri very fast and conveniently. So when I search for (parts of) a title, for an author and year, or for combinations of that from the normal Siri interface, the file is found promptly. I can then edit it with any PDF app I choose (PDF expert is perfect for that) and the changes are saved and reliably synced back via iCloud to my computer without further interaction.

    This function at least partly relies on Zotero renaming PDFs on my computer according to the standard scheme (author’s last name – year – title). So even if the content of the PDF is not OCRed, it will still find what is being searched. But for all PDFs that contain text (not just scanned images of pages), full text search in the content works as well. What doesn’t work, however, is searching for Zotero’s tags, collections etc.

    It's not perfect, but gets the job done reliably without the tedious process of sending something forth and back between PC/Mac and iPad – and you can use whatever PDF annotation app suits you.
  • edited September 16, 2019
    How exactly have you stored your library on iCloud?

    If you mean you have stored the whole Zotero data directory in iCloud, that’s not safe, and you should move it out of there immediately.

    See here for details on how to store your attachment files in a cloud folder safely:
  • edited September 16, 2019
    In the Zotero app go to the preferences menu. Then under the "Advanced" tab, there is another tab called "Files and Folders". Under "Data Directory Location", change to "Custom" and choose an appropriate folder on your iCloud drive.

    I am not sure if I first copied the library to that folder prior to changing settings or if I just changed the settings let it download the library back again from Zotero storage. In any case: be sure to make a backup first ;)...

    It also makes sense to check first how big your library is and whether you have enough space on iCloud.
  • No, as bwiernik says, and as the link documentation page says, you absolutely shouldn't that. Storing the data directory in cloud storage is extremely likely to corrupt the database.
  • Thanks for pointing this out dstillman and bwiernik!

    I used it for quite a while now this way without a problem – probably because I don’t use iCloud to sync the database to two instances of Zotero (I still pay for Zotero storage for this), but just to access the PDFs. However, that case has been covered in one of the threads mentioned in the documentation, stating it would decrease the risk, but not to zero.

    I’ll heed your advice and roll that config back and try to go the route via symlink (mentioned in the documentation linked by bwiernik) to get just the storage on iCloud but keep the database off cloud storage.
  • guys, i'm confused now.

    i have my database on my iMac
    but the zotero storage folder on my in my icloud drive.

    is this bad or what?
    erf ...
    this way i can just open the pdf on my ipad and
    back on my computer i can handle the annotations
  • What exactly do you mean by your Zotero storage folder in iCloud? How exactly did you set that up?
  • edited April 13, 2021
    I agree if the library could just be stored in iCloud somehow they can be opened through Files folder on iOS. The corruption issue was reported at my uni with Endnote cloud backups too - must be some data packet sync process issue breaking it up.

    I am very interested in the Zotero app mentioned 2 years ago above. Please please PLEASE, xx. I know you are busy supporting the desktop version and appreciate it and support Zotero by paying for the upgrade.

    I have spent hours trying to get this to work on the iPad so I can hand annotate, work when I commute and have spare time travelling in the car. It blows my mind that in 2021 the iPad and it's wonderful pencil annotation features have not been better developed by someone. I have tried Notability and Goodnotes (£10 each) and the experience is only fair to good. Tying or copy-pasting anything lengthy for research is not great but the OCR on handwriting is fantastic. I write a keyword in the margin like ESSAY1 and finding them all when writing up is Magic and worth it the effort.

    I can open in Goodnotes and Export to Papership and seems to work and keep my annotations. full steps here
    The text limitations are still an issue. I just want to keep all my files in one place so I can find them. When doing research there are a lot of files and Evernote is not adequate so I am still stressing over it.

    Anyone using Zotfile successfully?

    So much time hope it yields more fruit.

    Thanks in advance.
  • edited April 19, 2021
    oooooo thank you will sign up asap!
  • So y’all know PaperShip allows annotations right?
  • @stevejoslyn PaperShip is essentially dead. It receives almost no development support and does not sync reliably. As Dan notes above, the Zotero iOS app is in beta.
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