Managing Reference Data with Zotero: Annotating with the built-in PDF Reader

Viewing and annotating PDFs

When you double click a PDF file, it opens in an additional tab inside the Zotero window. You can have multiple PDF files open. You can go back and forth between the Zotero library and one or several PDFs.

• Highlights
  To highlight text in the PDF, select the "Highlight Text" button, mark the text, and select the desired color for the highlight. You can highlight text in 8 different colors. The highlighted text will automatically be copied into the annotations pane on the left. On the toolbar, the very left button, you can toggle the annotation Sidebar on or off as you wish.
• Sticky notes
  To add a sticky note with your own comments, select the "Add Note" button, click into the text where you want to add the note, and start typing. You can also add comment directly in the comment box to a highlighted text block when the Sidebar is on.   
• Image annotations
  To annotate a chart or image from the PDF, use the "Select Area" button, and drag your cursor over the area of the chart or image. Annotated images are saved as files within your Zotero data directory and synced the same as other attachment files. They count against your file storage quota. I have found the image resolution is not affected by how the PDF is Zoomed in/out.

Clean up metadata for items while viewing your PDFs

In the upper right-hand corner of the PDF reader, there are two buttons. The left is Item button.

• Click on it, it opens up the item details pane.
• As many articles include bibliographic information on the first page, this will assist you in verifying and cleaning up the metadata that was imported by Zotero.

Tips and tricks

• Adjust page number(s)
  If you need to adjust the page number(s), click on the vertical ellipsis next to your annotation or note, select "Edit Page Number," and change it to the appropriate number or range. 
• Annotations, sticky notes, and image annotations are save automatically. 
• Zotero stores PDF annotations in its Zotero database, not the PDF file itself. 
  • This makes it easier to synchronize annotations for PDFs shared within a group.
  • Annotations do not appear when the PDF is opened in an external PDF reader.
  • You can export a copy of the PDF with annotations embedded by using File → “Export PDF…” from the library view or “Save As…” from the PDF reader.
  • PDF annotations added in an external PDF reader will appear read-only (i.e. with a lock icon next to the annotations in the annotation Sidebar) in the Zotero PDF reader, but can be imported into Zotero by selecting File -> "Import Annotations...". After importing, the annotations will be editable.