Citation Management with Zotero

With Zotero 7, EPUBs now open in Zotero’s built-in reader in the same way as PDFs, and you can annotate them and add those annotations to notes just as you’ve been able to for PDFs. Additionally, webpage snapshots on news articles and other pages now open automatically in the reader, enabling you to annotate webpages as easily as PDFs.

Zotero 7 also makes available new annotation types, including creating ink, underline, and text annotations.

• Ink annotations were already supported on iOS, and it’s now possible to create them in the desktop app as well. (This works best if you have a touchscreen PC or stylus.)
• Underline annotations work just like highlights, while text annotations allow you to add text directly to the page.
• Underline annotations are available for PDFs, EPUBs, and snapshots, while ink and text annotations are available for PDFs only.

To maximize the value of the annotation features, your files should be stored on the zotero.org server. This will enable you to view your annotations in the Zotero Standalone, on the Zotero site, and on mobile apps. Zotero stores data automatically, as long as your account is set up to sync. See the Getting Started with Zotero tab to the left for more info.

You can view and annotate files inside Zotero by double-clicking on the reference or file in your library. Files open in a separate tab.

Annotation tools are in the center of the toolbar above the document. These include highlight text, underline text, note annotation, add text, select area notes, and draw. The tools offer eight color options.

The image below shows examples of annotations in a variety of colors.

If you open it, the sidebar (top left, above article) will display your annotations automatically, and you can use them to navigate the document. 

To view your annotations within the Zotero Standalone (as opposed to opening individual files), select the file you annotated beneath its reference in the Reference Pane (middle pane). Your annotations will display to the right.

Zotero allows you to add all annotations to a single note. Right-click the annotated file in the Center Pane. Click Add Note from Annotation.

The note will appear to the right, allowing you to add, edit, and format text, just like a Word doc.

The note is stored as an attachment under the reference in the Center Pane. Note titles can be modified.

Annotations are part of the Zotero metadata associated with your PDF, so if you view the original file on your computer, you won't see any. In this way, you can maintain a clean copy of the file while still annotating for your own use or to share in your group libraries. You also have the option of exporting a PDF with the annotations included, either by choosing Save as from the PDF reader or going to your library and choosing File ⇒ Export PDF.