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Zotero @ the WSU Libraries

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

Using ZotFile and Zotero to Sync and Annotate PDFs on a Tablet and Extract Annotations  (rev. 06/14/2016)

Note: This is about one particular functionality that the ZotFile plug-in offers for Zotero users – it does other cool stuff as well. To download ZotFile and/or read the official documentation, see: . 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; 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 to your computer (it will set itself up as a network drive). If you use another form of cloud storage, i.e. OneDrive, Google Drive, 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 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 [uodate: 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.

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). 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! 

Note: I highly recommend selecting the Additional Options that add a suffix to annotated files and extract annotations automatically (you can also extract annotations manually regardless of what PDF annotating service you use, i.e. Adobe Acrobat Reader on your laptop).

5.  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 article title (or the PDF attachment title). 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.

6.  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.pdf copy of the 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).                           

7.  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.

8.  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 to your Zotero library.  Your original PDF will still be there, along with a new PDF that includes your annotations – its title will have _annotated at the end before the .pdf extension. 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 have page numbers).

9.  Once the PDF has been downloaded back to its record in your laptop’s Zotero Library, it will be automatically deleted from PDF Expert and your Dropbox storage (it may take a minute).

10.  If you want to continue annotating a document that you have previously annotated, just repeat from Step 5, however instead of right–clicking on the Record name and Manage Annotations -> Send to Tablet  to send it to Dropbox/PDF Expert, you will want to right-click on the annotated version of the PDF. When you download the re-annotated PDF to its Zotero record, it will not replace the previously annotated files: you will now have a second annotated PDF that includes all annotations (this version’s title will end with _annotated_annotated.pdf), as well as a second updated Note that includes all extracted annotations that ZotFile was able to extract. 

Note: You will probably want to send the earlier annotated PDF and Note to the Trash to eliminate potential version control issues down the road. You may also want to delete the original PDF to save space; you can always print it out clean without your annotations/markups if you need to, or delete your annotations in your PDF app after the fact (you can also delete annotations made via the PDF Expert app using Adobe Acrobat Reader on your laptop).


Available in alternative formats on request; last revised: 6/14/2016 /loe Lorena O’English

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