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Zotero - Annotate PDFs - ZotFile

Learn how to manage highlighted quotes and annotations on a PDF document and collate these notes in Zotero using the Zotfile plugin for Zotero.

Zotero 6

Zotero 6 was released in March 2022. 

If you use an Android phone or tablet, you may still find Zotfile helpful for annotating PDFs on the go.

Need a quick Zotero refresher? Watch our workshop video.


Research & Annotations: Deciding if you need Zotfile

What is Zotfile? 

It is a third-party plug-in to Zotero that allows you to highlight quotes within PDF articles and add notes (annotate) PDFs saved to your Zotero Library and extract those to notes attached to your citations.

It also allows you to rename, organize, and synchronize attachments to items in your Zotero library. These organization features are especially useful for advanced users who plan on saving a large amount (over 200) PDF articles to their Zotero library. The free cloud storage offered by Zotero is usually enough for most users. 

How could Zotfile help you in your research process? 

Here are a few things to consider before installing and setting up the connections between your Zotero, Zotfile, PDF reader/annotation software, your cloud storage system, your mobile devices, and your computer.

  • Are you comfortable with computer settings and working "in the cloud"? If you prefer the physical process of note-taking, marking up articles by hand, and organizing print files, it may not be helpful to embark on a completely new and electronic system for organizing your notes and annotating articles. 
  • Do you find yourself reading articles online more often? If so, you may want to have your quotes and notes handy in Zotero while you're typing up your dissertation or paper. Zotfile works with your PDF annotation software and your cloud storage to save your thoughts & collate quotes you will cite in papers, projects, presentations, and class discussions. If you generally prefer annotating & highlighting on paper, than Zotfile may not be the right tool for you.
  • Do you need to read articles on an Android mobile device (i.e. a tablet or smart phone)? If you share a computer or would like the convenience of highlighting, annotating, and reading on a tablet, then Zotfile will help you import your notes & annotations into Zotero. 

General Advice

Consider what you currently use for cloud storage and research how that platform (Dropbox, OneDrive, etc.) would sync with your computer's files and with your mobile device. Consider if you'll continue to have access to that cloud storage once you graduate. For example, I am using OneDrive through the University of Redlands. If I change schools, will I still have access to these files? Probably not. 

Research what PDF annotation software works for you (more info in the PDF Annotation tab in the left menu on this page). When I realized that the OneDrive app for Kindle Fire allowed me to annotate PDFs, I appreciated not having to install another app. I can also annotate on any computer that has Adobe PDF reader software with annotation capabilities. In short, considering the devices you're using and the apps/software available to you, will you be able to annotate easily and in all circumstances?