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Zotero @ the WSU Libraries

Using Zotfile and Zotero to Sync and Annotate PDFs on a Tablet and Extract Annotations to Zotero Notes

Note: This is about one particular functionality that the ZotFile plug-in offers for Zotero users – it does other cool stuff as well.

ZotFile is freeware, but if you like it, you may want to donate to the creator. ZotFile works with both iOS and Android tablets, but you can also use some of its functionality even if you don’t have a tablet.

iPad users who use other iOS Zotero apps such as PaperShip: If you use PaperShip, you don't need to use the syncing functionality of ZotFile as you can access and annotate your PDFs via your iPad (of course, you can also do this directly at via your tablet's browser); however, you may still want to install it on your computer to use for things like extracting PDF annotations to a Zotero Note.  

  1. Download Dropbox/Google Drive/OneDrive/ your computer (it will set itself up as a network drive). If you use another form of cloud storage, i.e.  SugarSync, or Box, there should be something similar (a drive or folder) that allows you to sync files between your computer and the service.
  2. Make sure your cloud storage account is connected to your tablet’s PDF app (PDF Expert, iAnnotate, etc.).
  3. Create a folder in Dropbox/etc on your computer to store PDFs you want to sync to your tablet so that you can read and/or annotate them there via your PDF app and then return them to your computer’s Zotero library. This how-to will use Dropbox and PDF Expert on an iPad as examples from now on, but the experience should be similar for alternative cloud storage tools and PDF annotating apps. My sync folder is called Zotfile-FilesForZotero - I’m actually using the same Dropbox folder for syncing PDFs to PDF Expert that I use to store PDF files that are linked to their Zotero record via Dropbox rather than stored on Zotero’s online storage, but that is not required.
    • Note: this is actually a lie as I don’t really do that other than for testing purposes – I pay $20/year [update: I upgraded to $60, but still a bargain!] for Zotero storage for my PDFs which is very convenient and helps to support Zotero. I really recommend you use their storage rather than using a cloud service to store linked PDF files - not only does it help support Zotero, but it also saves your Zotero Snapshots.
  4. Download and configure Zotfile (you can set up your preferences either from Zotero Preferences’ Action drop-down menu or from your browser add-ons/extensions). I have a YouTube video that goes though the installation process for Zotfile (its a little complicated) and demos how to use it to extract PDF annotations.  Select the Tablet Settings tab and locate and select your syncing folder in the Base Folder browse box. Note the other cool things that Zotfile can do!
  1. Now that you have set up the connection between (in this case) your Zotero library, Dropbox, and PDF Expert on your iPad, you are ready to start syncing, reading, and annotating! In your Zotero library, go to the item record you are interested in, and right-click on the the PDF attachment title child file. From Manage Attachments, choose Send to Tablet. It may take a minute or so to upload to Dropbox and PDF Expert if your connection speed is low.
  2. Open PDF Expert and go to the Documents folder. Navigate to your Dropbox syncing folder and locate your Zotero folder, in this case Zotfile-FilesForZotero. You will see your PDF in the folder, and you can open it and annotate it in-app. Keep in mind that Zotfile will extract highlighted text (in quotation marks, with (author year:page(s)) added), as well as underlining (in quotations, underlined, with (author year:page(s)) added); it will also capture pop-up notes with your comments (your text plus page(s)). Any other annotations you make (sound, strikeout, typing, etc.) will not be extracted, although they will remain on the annotated article (and as noted below, you can opt to print out your document clean, without markups).
    • Note:  Different PDF reading/annotating apps may provide different functionality; for example, a PDF annotated with Adobe Acrobat Reader will also let Zotfile extract Add Note to Text, which will include both highlighted text with (author date:page) and your connected comment note in italics with the page number).                           
  3. Once you have completed your reading/annotation, close the PDF in your PDF reading app.  It may take a minute for the annotated file to sync, especially if you do not have a very fast Internet connection. If you have not yet enabled two-way syncing for that folder, do it now 
  4. From the record in your Zotero library, right-click on the title (record or PDF) and select Manage Attachments -> Get from Tablet to sync your annotated PDF back to your Zotero library.   A new dated Note will show up that includes all the annotations that ZotFile was able to extract, with author, year, and page number(s) included (your note annotations will also include page numbers). Note: if Zotfile doesn't extract your annotation, sometimes the file didn't do that last sync. If you go to your cloud storage folder and click on the PDF article link that should finish the sync and allow you to extract your annotations.
  5. Once the annotated PDF has been downloaded back to its record in your laptop’s Zotero Library, depending on your settings it will either be automatically deleted from PDF Expert and your Dropbox storage (it may take a minute) or it will remain on your tablet.
  6. If you want to continue annotating a document that you have previously annotated, if you deleted it from your tablet  after extracting the annotations last time you worked with it, just repeat from Step 5, .Actually I recommend always deleting it from your tablet after you have finished annotating, and then re-sending it to your tablet. when you are ready to continue annotating. I tested it out with the saved copy on my tablet, and it did not always sync my annotations to the document once I synced the file back to Zotero  (I think there is a process/pattern to make it work but I have not yet figured it out). When you extract your Notes this will extract a new dated Note that includes all extracted annotations that Zotfile was able to extract, including previously extracted annotations as well as your new annotations.. Important Note: if you have added (type ) comments/additions on the original extracted Note from inside Zotero, you don't want to delete the older note because you will lose your Zotero-created additions to the original extracted annotations that are included in that Note. I recommend copying and pasting the newer extracted notes into the original Note at their appropriate location based on their content or the page they were extracted from. 

Note:  Your PDF will now have annotations  on it, but there may be times when you want to print it out without your annotations.  On my Windows machine using Adobe Acrobat Reader (or whatever its called this week) you can always print it out clean without your annotations/markups if you need to - look at the drop-down menu with the title Comments & Forms - it will let you print your document without markups (you can also delete annotations made via the PDF Expert or other pdf annotation tool using Adobe Acrobat Reader on your laptop, print out the document, then close the PDF without saving it).

Note: As of 2/4/2021, Zotfile's options to "save a copy of the annotated file with suffix _annotated" and "automatically extract annotations wihen getting PDF back from tablet" are not working, even if selected, so they are not included in this guide.

Available in alternative formats on request; last revised: 2/4/2021 Lorena O’English 

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