Zotero

As of version 6, Zotero has its own built-in PDF editor that can be used to annotate PDFs. If you use another program to edit PDFs, Zotero will still save the annotations you make from PDFs in other programs, such as Adobe Acrobat.

To enter Zotero's PDF editor, double click a PDF or the reference that the PDF is attached to.

Clicking the button in the top-left (left of the magnifying glasses) will show a list of all the annotations currently in the document. There are many different annotations you can make:

1. This annotation with a 'lock' icon in the top-right part of the box was already on the document and made in another editor. You won't be able to edit or delete it in Zotero's built in editor, but you can still view it.
2. You can use the 'Add Note' tool to place this sticky note icon anywhere on the page to add a comment for that area in general.
3. You can use the 'Highlight Text' tool to highlight text comment on the text of your choice. Sometimes, the highlighter has trouble picking up spaces between words, and you may need to edit the quote by clicking inside the annotation box on the left hand side.
4. You can use the 'Select Area' tool to capture and comment on an image of the selected area. Although I used it on text here, this tool was designed to be used with images, charts, and other tables that aren't captured well using the highlighter.
5. 'Item Notes' on the right tab are notes about the document as a whole, and aren't linked to certain text, sections, or pages.
6. You can also consolidate all your annotations onto one Item Note by returning to the list of references, right clicking your PDF, and choosing 'Add Note from Annotations'. This is mostly used to export your annotations to markdown editors such as Obsidian. Doing so will make your annotations searchable from the Zotero Library search bar, which can be very useful!

Zotfile is an open source plugin for Zotero that can automatically extract annotations and save them in a Zotero note. You can use this to keep track of quotes you wish to cite, or important ideas to remember without opening the PDF directly, but Zotero 6 aleady does this. Zotfile can also be used to automatically batch rename and move attachments, and sync PDF's with a tablet.

1. Download the Zotfile plugin from http://zotfile.com/
2. Install Zotfile in Zotero
   • Open Zotero and choose Tools > Addons from the menu in the top left
   • In the new window that appears, click the gear in the top right and choose "Install Add-On From File..." and select the file you downloaded from Zotfile
   • Restart Zotero
3. Right click your annotated PDF in Zotero or it's parent element and choose "Manage Attachments > Extract Annotations". A new note will appear that contains all your PDF annotations with the date and links to that page in the text.

If you want to edit Zotfile preferences, they can be found under "Tools > Zotfile Preferences..."