Zotero released version 6.0, which includes many new features.
In preferences, you have the ability to open PDFs using the program you've designated as your System Default, or browse for another program on your computer. In Zotero 6.0 you can choose to open them with Zotero.
The PDF opens up in a tabbed interface.
In the menu that appears in the upper right-hand corner, the first option opens up the item details pane. As many articles include bibliographic information on the first page, this will assist you in verifying the metadata that was imported by Zotero.
The second option opens up a notes panel. Click on the + and choose to add a new note, which will open up the note editing window. The other option is to Add Item Note from Annotations.
In Zotero's PDF viewer, you can highlight text and add comments, and add tags to your comments. If you then choose the option Add Item Note from Annotations, the highlighted text and comments are extracted and put into the notes pane.
The annotations are automatically saved. Like all Zotero library data, the annotations you create will automatically sync across all your Zotero installations. You can also create PDF annotations in group libraries.
The annotations in the notes include live links that will return you to the place in the PDF where you made the annotation.
It will always remain possible to set Zotero to open PDFs in an external reader if you prefer one to the internal reader. Externally created highlights and notes show up in the PDF reader and can be added to Zotero notes as easily as annotations you create in Zotero. Right click on the PDF attached to the item in your library and choose Add Note From Annotations from the menu.
In Microsoft Word and in Google Docs, an "Add Note" button has been included in the Zotero menu.
When you choose Add Note, Zotero will prompt you to first choose a citation style. Then a list of notes will appear, which you can choose from. The annotations in that note will be inserted into the document, along with a citation to the original document.
The PDF reader syncs seamlessly with the Zotero iOS app, allowing you to highlight and take notes on your iPad or iPhone and then quickly pull those annotations into a note or word processor document when you're back at your computer. PDFs will open automatically to your current page, no matter what device you last used.
In addition to natively supporting annotations and citations, Zotero notes now fully support embedded images. You can drag in images from your computer or the web, and they’ll sync to your other devices. You can also create an “image annotation” in the PDF reader and drag it straight into a note to easily create a cited image in your document.