Citation Management with Zotero

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

The details pane opens automatically, defaulting to the reference's Info tab.

You can open the left-hand sidebar by tapping the arrow icon at the top left of the toolbar. This allows you to view your annotations as you create them, as well as the PDF's pages and outline (if available).

Annotation tools are in the center of the toolbar above the document. These include highlighting, sticky notes, and selecting areas (essentially a screenshot). The tools offer eight color options.

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

If you open it, the sidebar will display your annotations automatically, and you can use them to navigate the document. You can also filter by annotation color.

To create and view notes from your annotations, tap the notebook icon at the top right of the details pane to switch to the notes pane.

You can create a note from an existing annotation or all existing annotations at once. You can also add annotations to existing notes. Any notes you create here will show up as attachments to the references in your library.

Create a blank note

In the notes pane, under Item Notes, tap the plus sign (+) and choose Add Item Note. Notes operate much like Word documents, with the options to format text and add links. You can also drag and drop images into a note. As with notes in your library, you can add tags at the bottom.

Create a note from annotations

Once you've added annotations to your PDF, tap the plus sign (+) in the notes pane and choose Add Item Note From Annotations.

Your existing annotations will now appear in the note with their citations. If you add more annotations later and wish to include them in the same note, select it in the notes pane and right-click the annotation. You can also simply drag and drop the new annotation into the note. Below is a sample note created from annotations.

By default, notes display only the text (not the color) of an annotation, as well as its citation. If you wish to display annotation colors or hide citations, tap the note in the notes pane. On the toolbar above the note text, tap the three horizontal dots all the way to the right. Here you can select Show Annotation Colors and/or Hide Annotation Citations.

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.

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 client, on the Zotero site, and on the iOS app. If you store your data elsewhere, such as on your OneDrive, you'll see your annotations in the Zotero client on your computer, but not elsewhere.