From reading to citing: the new Zotero workflow

Desk, notepad, laptop and smartphone

Big news for Zotero addicts! Version 6 was released along with an iOS app for iPhones and iPads. They should make your writing workflow smoother, from PDF management to notes and citations. Join us on a guided tour of the new options and a reminder of how notes can play a central role in your workflow.

First, some reassurance: you will not lose your bearings, and the basic features (how to add a reference, organize your library, cite) have not changed.

Built-in PDF reader

Zotero is more than a database of bibliographic references: it automatically fetches the full text of articles and attaches it to the references. Files (including PDF) can also be attached manually if necessary.

Until Zotero 6, users had to use external readers to work on their PDF files. This gap has been filled, and Zotero now includes a PDF reader, which opens in an additional tab inside the Zotero window, allowing you to go back and forth between the Zotero library and one or several PDFs. Annotation and highlighting tools are available with 5 different colours, and two lateral panes allow visualising the document’s Zotero record if you need to correct the metadata, but also the annotations and highlighted parts and any note in the Zotero library.

Annotations evolved

If you made some annotations in external readers before the release of Zotero 6, you will still find them in the Zotero reader as read-only. To make them editable, you can transfer them into Zotero (select File -> “Import Annotations…” from within the PDF reader).

Some users may be surprised not to find their annotations again if they open a PDF outside of Zotero. Indeed, they are not stored in the PDF file but in Zotero itself, which can be disturbing. This option makes it easier to synchronize annotations in documents shared within a group, but a critic qualified it as “a form of vendor lock-in”. Zotero insists that data portability is one of its founding principles and users can export their PDFs with the annotations embedded if they wish to use another PDF reader.

From PDF to notes

You can extract your annotations or highlighted passages to include them in a note within your Zotero library. The note editor now includes many additional features to format text and add hyperlinks or citations. They also include direct links to the annotated/highlighted part of the original text.

Zotero is not just a citation manager. Notes do not have to be attached to references and can be standalone – a convenient way to store ideas and thoughts that emerge during your work. All notes can be tagged and linked to other notes or references using the “related” tab.

Read and annotate wherever you are

Your annotations will synchronize across all your devices, including smartphones and tablets.

If you have an iPhone or an iPad, you can install the new app, read and annotate your texts on your mobile device and return to your laptop without losing anything. You will not even need to close the PDF, and it will open automatically on the last consulted page. You can also share annotations with your colleagues in group libraries.

Owners of Android devices also have options such as synchronising their PDFs with their tablet using Zotfile.

From notes to final text

Last but not least, the Zotero toolbar now displays a new button to insert the content of notes directly into a text. You may need to reinstall the Word or LibreOffice add-in to make it appear.

Your reading/annotating/writing workflow can now run smoothly, allowing you to concentrate on the intellectual part of the work.


Our Zotero libguide was updated to include these new features. If you still have some issues or questions, do not hesitate to contact Catherine!

Illustration: picture by Firmbee (Pixabay license)

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