Zotero to manage references and literature notes

A reference manager can be simple or it can be complicated. It can be free or it can be a paid product. It can be open-source or it can be proprietary.

Personally, I have gravitated toward Zotero as a reference manager for a few reasons:

  • free
  • open-source
  • web plugin to allow easy retrieval of reference and PDFs
  • can integrate with LibreOffice (if I must)
  • renames my PDFs
  • maintains a current BibTeX file of my references
  • plugins allow additional functionality

Most people are familiar with what a reference manager does, and the Zotero website has easy-to-follow documentation if ever you get stuck. However, I wanted to point out a few things I have found helpful.

Retrieving references and PDFs

We can import many types of references files into Zotero. However, most of the time, I retrieve my references as I search PubMed or similar databases.

We can download and install a Zotero plugin for our browser to retrieve references and PDFs. If we just completed a search on PubMed and we click on the Zotero plugin (with the Zotero Desktop App running), we are presented with a window that allows us to select the references we might want to download.

Alternatively, if we have a single reference highlighted, we can download the reference (and possibly the PDF). This works when we are searching on PubMed and when we are searching on a publisher’s website. We might have signed up to receive the Table of Contents of a journal we like. When we receive a notice and we see a paper that might be of interest, we can click on the link, go to the publisher’s website and easily retrieve the reference and PDF.

Organising PDFs

I store my PDFs on my computer and use Zotero to rename the files. This can be done automatically, and with whatever format we like. Personally, I have found the Zotfile plugin a great help here.

Useful tools

Zotero has some great built-in tools, which are all well documented. However, we can add tools to Zotero by adding plugins written by friendly Zotero users. I would like to highlight three plugins that I have come to love.

The first plugin, Zotfile, was mentioned above. It helps manage our PDFs.

The second plugin is Better BibTeX. It provides several nice tools for those of us who like to work with BibTeX.

The final plugin is Mdnotes. It allows us to export metadata and notes to Markdown format.

Personally, I like to highlight key passages in papers I read. Zotfile can actually extract the highlighted text and Mdnotes can convert it to Markdown. This is very useful for anyone working with the Zettelkasten approach to taking smart notes.

Similarly, I use Mdnotes to write notes about the papers I read. These notes are insights I have when reading papers, insights I would surely forget if I did not write them down. What is great is that I can store them as Markdown files alongside my PDF files, and Zotero will make it clear that I have notes for a given paper.


No reference manager is perfect, no matter how much it costs (to you, or your institution). If you are starting out, I recommend not getting roped into a proprietary reference manager. After lots of trial and error, I have come to enjoy using Zotero as part of my daily workflow. Maybe you will grow to enjoy it as well.

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