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Zotero

Highlighting, Annotating

Zotero 6 (released in March 2022) has a built-in PDF reader, allowing users to open PDFs in a new tab, navigate easily between PDFs and library, highlight, annotate them, add comments or tags to the highlighted parts and the annotations, and extract the annotations in a note. Links in the annotations allow finding quickly the place in the PDF document with the highlighted sentence or the note.

Notes are not stored in the PDF file but in Zotero itself. They do not appear if the PDF is opened in an external PDF reader. It makes it easier to synchronize annotations for PDFs shared inside a group. But it is possible to export a copy of the PDF with the annotations embedded (File -> Export PDF from the library view or "Save as" from the PDF reader) and then go on working on it outside of Zotero.

PDFs annotations added in an external PDF reader appear in the Zotero PDF reader as read-only, but they can be transferred into Zotero by selecting File -> "Import Annotations..." from within the PDF reader, after which they are fully editable.

Zotfile

Zotfile is a Zotero plugin to manage your PDF attachments: automatically rename, move, and attach PDFs (or other files) to Zotero items, sync PDFs from your Zotero library to your (mobile) PDF reader (Ipad, Android tablet...).