Zotero

Zotero has a built-in PDF viewer that allows you to highlight text, add sticky notes, and even create snapshots of images, charts, etc. You can also conveniently extract these annotations as a Zotero note. 

To open a PDF in the viewer, simply double-click on the item record, or on the PDF attachment. 

Highlights 

To highlight text in the PDF, select the "Highlight Text" button, mark the text, and select the desired color for the highlight. The highlighted text will automatically be copied into the annotations pane on the left.

Sticky Notes 

To add a sticky note with your own comments, select the "Add Note" button (it looks like a piece of paper), click into the text where you would like to add the note, and start typing.

Snapshots 

To select a chart or image from the PDF, use the "Select Area" button and drag your cursor across the area you would like to screenshot.

All of your annotations, sticky notes, and snapshot should be saved automatically and will sync with your online Zotero library, as long as you have set up syncing. 

Important: Make sure that your annotations, notes, and snapshots refer to the correct page number. If you need to adjust the page number(s), click on the kabob/vertical ellipsis next to your annotation or note, select "Edit Page Number," and change it to the appropriate number or range. 

You can use Zotero's notes functionality in several different ways: 

• Manually add notes, either to a particular citation record or stand-alone notes.  
• Create notes from websites. 
• Extract annotations and comments from PDFs. 

Add Notes Manually 

To add notes to items in your Zotero library:

1. Select the item you want to add a note to. 
2. Either 
   • Click on the Notes icon on the far right and click on the "+" button.  
   • Or right-click on the item in the center pane and select "Add Note." 
   • Or click on the Add Note icon in the menu across the top (it looks like a sticky note) and select "New Item Note."
3. The note editor will display. 
   If you prefer to write your note in a pop-out window, click on the ellipsis in the top right corner of the note and select "Edit in a Separate Window." 
4. Start typing your note. 

To add standalone notes: 

1. Navigate to the collection in which you'd like to create your note. 
2. Click on the Add Note icon in the menu across the top (it looks like a sticky note). 
3. Select "New Standalone Note." 
4. The note editor will display in the pane on the right. 
   If you prefer to write your note in a pop-out window, click on the ellipsis in the top right corner of the note and select "Edit in a Separate Window." 
5. Start typing your note. 

A few notes about the note editor: 

• Rich-text character and paragraph-level formatting is available under the icon with the letters Aa. This formatting will carry over into Word or Google Docs if you insert the notes via the "Add note" functionality of the Zotero plugin. 
• If you reference a specific item, or a specific passage of an item, in your note, consider using the "Insert Citation" option. This can be useful when inserting notes via the "Add Note" functionality in your word processor Zotero plugin because it will carry over the citation, similar to inserting citations by themselves. To insert the citation:
  1. Click on the "insert citation" icon (it looks like lines of text in between quotation marks). 
  2. Search for the item you're referencing in the floating red search box that will pop up. 
  3. Select the item from the list of search results. 
  4. Once the selected item appears in the red box, click on it again and enter any relevant page, chapter, or other references. 
  5. Hit enter to confirm and close the red box. 
• To rearrange sections/paragraphs within a note, simply hover over the left margin next to the section/paragraph until your cursor turns into a hand icon. You can then drag the section/paragraph around without needing to copy and paste. 
• Good to know: Your note will save automatically; you don't need to click on a save button. 

Create Notes while Browsing the Web

With Zotero, you can also create notes directly from webpages you visit.

1. Highlight the text you want to copy into a note. 
2. Right-click (ctrl-click on a Mac) and find the Zotero option in the context menu. (In Firefox, it is labeled "Zotero Connector"; in Chrome, it is labeled "Save to Zotero.")
3. Follow the menu to the option to “Create Zotero Item and Note from Selection."

In Firefox, this will take two steps through the menu:  

 

In Chrome, this will take only one further step:  

You will now have a new item in your Zotero library, with a note containing the selected text: 

Extract Notes from PDF Highlights and Annotations 

Zotero also allows you to extract highlights and annotations saved in a PDF as Zotero notes, which makes them fully searchable and easier to organize. (For detailed instructions on how this works, please check the section Annotate PDFS on this guide.)  

To extract annotations from the PDF, return to the library view, select the item, right-click, and select "Add Note from Annotations." 

This will generate a note that copies all of your highlights, notes, and screenshots you have added to the PDF at this time.

If you add additional annotations later, you can repeat this process and generate a new, more complete note if you wish.