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The Best Reference Manager Setup
(Zotero 7 + ZotMoov + Cloud Storage)
By: Stephen Chignell
https://www.researchgate.net/profile/Stephen-Chignell
Last updated: November 4, 2024
Contents
Introduction ..................................................................................................................................................................................... 2
Part 0: Switching to Zotero ........................................................................................................................................................ 3
Part 1: Install Zotero and the Zotero Connector ................................................................................................................ 4
Part 2: Install a cloud storage service ..................................................................................................................................... 5
Part 3: Install and configure ZotMoov ................................................................................................................................... 5
Set up PDF syncing ................................................................................................................................................................... 6
Stop automatic PDF syncing to Zotero Cloud ............................................................................................................... 7
File renaming (optional) ......................................................................................................................................................... 9
Syncing across multiple devices (optional) ..................................................................................................................... 9
Part 4: Install other plugins ...................................................................................................................................................... 10
Part 5: Getting papers in and out of Zotero ...................................................................................................................... 10
Adding items with the Browser Connector ................................................................................................................... 10
References vs. Attachments ................................................................................................................................................ 12
Deleting items .......................................................................................................................................................................... 13
Using Zotero with Word processors ................................................................................................................................ 14
Part 6: Annotating with Zotero ............................................................................................................................................... 14
Using Zotero’s annotation system .................................................................................................................................... 14
Extracting Annotations to Notes ....................................................................................................................................... 16
Importing Annotations ......................................................................................................................................................... 17
Part 7: Adding Lookup Engines .............................................................................................................................................. 17
The Locate Button ................................................................................................................................................................... 17
URL Resolver ............................................................................................................................................................................. 18
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Part 8: Miscellaneous tips & tricks ........................................................................................................................................ 19
Various ways to add references to Zotero .................................................................................................................... 19
Showing Items in Subcollections (a.k.a. recursive folders) ...................................................................................... 21
Searching the Library ............................................................................................................................................................. 21
Deleting PubMed entries ..................................................................................................................................................... 21
RSS Feeds ................................................................................................................................................................................... 21
Groups ......................................................................................................................................................................................... 21
Introduction
I wrote this tutorial because after years of using Mendeley (and then Zotero with default settings) I
figured out a system for reference management that is extremely smooth, efficient, and free. It has
improved both my research and writing process so much that I wanted to share it with others.
The key is to use Zotero with ZotMoov (a free plugin), and a cloud-based storage service (e.g. DropBox),
in addition to a few minor changes to Zotero’s settings. By the end of this tutorial you will be able to:
• Download, rename, and organize academic papers, news articles, web sites, and other reference
material with one click.
• Have virtually unlimited storage for your PDFs with automatic back up.
• Make notes and highlights in your PDFs, and extract these as annotations for future references,
searching, and additional note taking
• Search and insert references within a Word document and automatically insert a reference list in
the required formatting style of virtually any journal.
• Create multiple group libraries that you can share with collaborators and/or the public.
Why Zotero?
• Free and open source
• Powerful and flexible
• Active user community
PC/Mac?
Although this tutorial is written from a Windows perspective, all the essential steps should work on a
Mac. Some things in the screenshots and configuration options might be slightly different from what is
pictured in the tutorial, but it shouldn’t be too difficult to figure out.
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Part 0: Switching to Zotero
Many people may be in a situation where they have already invested a lot of time and money into a
proprietary reference manager such as EndNote or Mendeley. I used Mendeley for a couple of years
before it was bought by Elsevier, who have since moved toward commercializing the software (which is
one of a several reasons why I decided to ditch them).
As far as I know, there are three options for migrating your existing reference library over to Zotero:
1) Exporting your references from EndNote or Mendeley into Zotero is very easy. There are
instructions for exporting from EndNote (here and here) and Mendeley (here, here and here).
2) Exporting your references + PDFs might be a little more work, but shouldn’t be too difficult.
3) Exporting your references, PDFs, subfolders, and annotations is more challenging, but
definitely possible (I know because I did it myself!). I think Menotexport is probably the best way
to do this from Mendeley, but there are other options out there as well.
a. Note that as of October 29, 2024, Zotero includes the ability to import directly from
Mendeley. However, a couple of years ago Mendeley moved toward encrypting their
database and PDFs, so may have to follow the workaround in the above link. Even then,
your PDFs may be “locked” for editing outside of Mendeley, although I haven’t tested
this in recent years.
4) When doing a large import, Zotero may try to automatically find the associated metadata for
each paper via Google Scholar. However, after a couple hundred of requests, Google will
suspect you are a bot and automatically put up a CAPTCHA, which may slow or stop the import
process. To avoid this, simply disable your internet connection during the bulk import; you can
always go back and tell Zotero to look up citation information for specific files later.
Finally, although I’m confident in this Zotero setup, I recommend going through the rest of the tutorial
and trying out Zotero before doing any migrations, just to make sure you like it.
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Part 1: Install Zotero and the Zotero Connector
1) Download and install Zotero 7 (desktop app) and the Zotero Connector (browser add-on)
2) Turn off automatic screenshots (optional)
a. By default, Zotero will make a copy of the web page and attach it to the record in your
Zotero library. Some people like this feature, but I prefer to only attach PDFs.
b. To turn this feature off, go to the top menu bar (in the Zotero desktop app) and select
Edit → Settings. In the pop-up window that appears, make sure the relevant box under
“File Handling” is unchecked:
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Part 2: Install a cloud storage service
1) Choose your service
a. This could be a service that you already have an account with (e.g., Dropbox, Google
Drive, ProtonDrive, etc.)
b. If you’re looking to maximize storage space, I recommend MEGA. Their free plan gives
you 20 GB (which is a lot of PDFs).
2) Download the desktop syncing app for your cloud service (e.g., MEGA Desktop App).
3) Go to the cloud service syncing folder on your computer and create a new folder. This is where
your PDFs will be stored, so you might want to give it an appropriate name like “Zotero” or
“Zotero_Library” (see below).
Part 3: Install and configure ZotMoov
ZotMoov is an excellent plugin for Zotero that helps to manage your PDFs by automatically linking and
reorganize your files. Note that this plugin is very similar to the plugin ZotFile, which is no longer
working with Zotero version 7.
1) Visit the ZotMoov site and download the latest release as an .xpi file (right click and choose
“Save link as” and save it somewhere on your computer)
2) In Zotero, go to the top menu bar and select Tools → Plugins
3) Click the gear icon and click “Install plugin from file”
4) Navigate to and select the .xpi file for ZotMoov that you downloaded
5) ZotMoov should then install, but you may need to restart Zotero
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Set up PDF syncing
Once ZotMoov is installed, go to the top menu bar in Zotero, and click Edit → Settings. In the pop-up
window select “ZotMoov” (you may need to restart Zotero first).
1) For Directory to Move Files To, choose the new folder you created in your cloud syncing app in
Part 2.
2) Set Source Folder for Attaching New Files to a folder of your choice. When you add a reference to
Zotero, ZotMoov will look to this folder for a PDF to associate it with
a. Your “Downloads” folder is a good option (this is what I use)
b. Some people might prefer to use a separate folder as holding tank (e.g. a folder on the
desktop called “Papers for Zotero”)
3) You can experiment with the other settings if you like, but here is what I use:
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You can instruct ZotMoov to organize your PDFs into subfolders by author name, year, journal name,
etc. (see the ZotMoov settings for more info). Personally, I find it more useful to store all of my PDFs in
one big folder on the synced cloud service folder (see below).
I then make subfolders within Zotero, since this is where I spend most of my time navigating. Note: If
you like subfolders, you may want to review the “Other Tips” part of this tutorial for instructions on how
to enable these within Zotero.
Stop automatic PDF syncing to Zotero Cloud
When you make a Zotero account on Zotero.org and start to sync your Zotero library with the Zotero
cloud, it will default to uploading your PDFs along with your references.
However, remember that we want to store the PDFs in “My Library” to a separate cloud service using
ZotMoov, so we need to change some settings before starting to sync:
1) Open the Zotero Preferences
2) Navigate to the Sync tab
3) Under File Syncing, uncheck “Sync attachment files in My Library using Zotero”
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This is the primary setting that you need to change in order to have your references sync to the Zotero
cloud, while your PDF attachments sync to your personal cloud service. Note that under the “Data
Syncing” options, you can choose whether to have Zotero sync your data automatically or manually (as I
do).
If you plan to collaborate with other Zotero users using group libraries, you’ll probably want to check
the box for “Sync attachment files in group libraries using Zotero storage” as I have in the screenshot
above.
To learn more about syncing with Zotero, I suggest reading the documentation (here).
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File renaming (optional)
Often the PDFs we download from a journal website have a confusing name. Zotero can automatically
rename PDF files to something meaningful like “AuthorLastname_Year”. You can adjust the settings for
this in the Zotero Settings under File Renaming.
Syncing across multiple devices (optional)
If you intend to sync across multiple devices, such as a work computer and a home laptop, you will
need to set up relative paths in the Linked Attachment Base Directory.
Go to Zotero Edit → Settings. Click on Advanced. Under Files and Folders set “Base Directory:” to the
folder you created in your cloud service desktop syncing app in Part 2. You will have to do this on each
of the computers you use.
Make sure to keep everything else in this window at default settings. In other words, keep the “Data
Directory Location” as the Default.
If you’re interested, you can find more information about these settings here and here.
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Part 4: Install other plugins
I highly recommend installing a Zotero Word Processor plugin (Microsoft Word or LibreOffice). There is
also a plugin for Google Docs.
There are many other plugins that are not required for the overarching setup to work but they will make
your life easier and improve the overall experience. I recommend visiting the official plugins page and
Mohamed Elashri’s list of awesome Zotero plugins, and trying a few out. Just follow the steps to
download and install the respective .xpi files, just as you did for ZotMoov.
Part 5: Getting papers in and out of Zotero
Adding items with the Browser Connector
You now have everything you need to start managing your references with Zotero. Zotero has many
built-in features and there are many resources online for learning about these. I’m therefore going to
focus on some of the particularities of this specific setup. Let’s start with an example.
Suppose you come across a paper that you would like to download. Let’s use this paper on
conservation narratives as an example (and shameless plug for my own research).
The first step is to open the Zotero app on your computer. Once Zotero is open, go back to the
browser and notice that the icon for the Zotero Connector (usually in the top-right corner of the
browser window) has changed to look like a manuscript (see below). This indicates that Zotero
recognizes that there is a reference on the web page, and that it is a journal article.
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If we were to click this button, Zotero would go to work grabbing the reference information from the
page and looking for an open access PDF to download. It would then appear in our library.
However, I want to be more organized and direct this reference to a subfolder (or “Collection”), not just
my general library. So before I click the button, I’m going to go back to Zotero and click the
button to create a new Collection. I’ll name it “Conservation”.
Now go back to the browser and click the Zotero button.
Watch and wait in wonder as the Zotero Connector grabs the reference and the PDF and saves it to the
“Conservation” collection in Zotero (below).
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If you switch back to Zotero you should see the reference (highlighted in blue below) and the link to
the attached PDF immediately underneath. The column on the right shows the detailed metadata,
which you can manually edit as needed.
Meanwhile, in the background, Zotero and ZotMoov have automatically taken the PDF, renamed it, and
moved it into the syncing folder on your cloud service. You can locate the original file by right clicking
and selecting “Show File”
References vs. Attachments
This is an important moment to note that Zotero makes a distinction between the reference (or parent
item) and the file(s) associated with it. If you wanted to, you could have a whole Zotero Library
composed of references, with no PDFs at all. You can also have PDFs in Zotero that have no associated
reference.
Continuing with our example, let’s say you find this book on Rights of Nature approaches to
conservation. The PDF is not available from the website, but you can still download the reference with
the Zotero Connector to your “Conservation” collection.
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As you can see below, Zotero now has the Book reference, but no attachment. The People and Nature
article, however, has a little PDF icon, showing it has an attachment.
Double-clicking on a reference will open the associated file.
If the reference does have a PDF attachment, Zotero will open it.
However, if the reference doesn’t have an attachment, Zotero will open the website where you found
the reference (try it with the book on the Rights of Nature).
Clicking the sync button in the top right corner will sync your references to your Zotero Cloud (you
will have to make an account first). Remember, this will only sync the references, not the PDFs. The latter
are being synced by your personal cloud service (e.g., MEGA).
Deleting items
To delete an item in your Library, just right click it and select “Move Item to Trash”. It will be moved to
your Trash folder within Zotero, and ZotMoov will delete the PDF file from your syncing folder
automatically once the Trash is emptied.
To delete a collection, right click on it. You can choose “Delete Collection”, which will just delete the
folder and leave the references in your library.
Alternatively you can choose “Delete Collection and Items” which will move them to Zotero’s Trash
folder.
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Using Zotero with Word processors
Given that adding citations and bibiliographies this is one of the primary functions of Zotero, I’m not
going to say much here, as it is very straightforward and there are plenty of resources demonstrating
how to do this (see here).
Part 6: Annotating with Zotero
Using Zotero’s annotation system
I think that one of the best parts of Zotero 7 is its built-in annotations system. However, if you already
have an app that you like for reading and annotating PDFs, you can still use that with Zotero—you just
need to tell Zotero to open attachments in that specific app. For doing so, you may find the Zotero
Open PDF plugin useful.
Otherwise, let’s explore Zotero’s built-in system using the paper we downloaded earlier. In your Library,
navigate to the ‘Conservation’ collection and double-click on the reference for Chignell and Satterfield
2023 to open the PDF in Zotero.
Notice that there are several tools at the top of the viewing window:
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Let’s use the default yellow marker to highlight some blocks of text in the document:
Maybe we see a figure we really like and want to remember for later. We can highlight the figure and
caption by choosing the Select Area tool and dragging a box around it:
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On the lefthand side, you can see that Zotero is tracking all of the
annotations as we go. This is very useful for organizing our thoughts
as we read through the rest paper,
perhaps changing the highlighting color,
trying the underline tool,
or placing free-standing sticky notes .
Extracting Annotations to Notes
Another powerful feature of this system is the ability to extract annotations embedded within a PDF into
a separate note file that is linked to the reference.
To do this, right-click on the reference in your Zotero Library and choose Add Note from Annotations.
You’ll see that Zotero has created a new Note file called ‘Annotations (date-time)’ and linked it to the
reference next to the PDF.
Selecting the note will bring up the side-bar with all of the annotations you made in the document.
These can be searched, added to, highlighted, etc.
Note that if you used different color highlights, you can display these by clicking the Note options
in the top-right corner and unchecking “Hide Annotation Colors”
Another feature that I really like is the ability to right click on any of the annotations and choose Show
on Page. Zotero will open the PDF and bring you right to the page where you made the note. This can
be extremely useful for tracking down a specific quote or point that you want to cite.
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There’s a lot you can do with Notes, and you can add even more functionality by downloading the
Better Notes plugin. I encourage you to check this out in more detail if you do a lot of note-taking.
Importing Annotations
If you have a PDF with existing annotations (e.g., you made highlights in Adobe Acrobat Reader), you
can also import these into Zotero’s system. Open the PDF in Zotero. From the top menu click File →
Import Annotations. Zotero will find and convert all the annotations for you (note: you may have to
unlock them to make them editable).
Part 7: Adding Lookup Engines
The following is optional, but it can be so useful that I’ve given it its own section.
The Locate Button
If you look on the righthand side of Zotero, you’ll see a “Locate” button . Clicking this gives you
different options for opening whichever reference is currently selected in your library.
This can be useful for locating the original website or URL or the associated record in your institution’s
library catalogue. However, these defaults are just the tip of the iceberg.
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1) Follow the instructions under "Managing Search Engines" on this webpage,
2) Navigate to your Zotero Data Directory. Mine is at C:\Users\steve\Zotero\locate and looks like
this:
3) Delete the default "engines.json" file and replace it with the one that I’ve provided here.
4) Close and restart Zotero.
5) Select a reference from your library and then click “Locate” .
6) You should see a variety of new options to choose from, including
Google Scholar, Web of Science, and Sci-Hub (right). These can be
extremely useful for quickly locating reference information and/or
PDFs from the internet.
Note: Not all search options will always be available. It will depend on what
type of reference it is, and whether it has a DOI listed in your Zotero library.
URL Resolver
You may also want to consider setting up an OpenURL resolver to help
identify references with the “Lookup” button. This can be very useful,
especially if your organization has a library that gives you access to journals.
Here are instructions.
You can quickly check if your organization has access by going into Zotero
Settings → General, and under Locate click the drop-down menu for
“Resolver:”
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Bote that sometimes these are out of date, so I’d recommend check your institution/library for the most
up-to-date link and enter it in the Base URL field as a custom URL.
Part 8: Miscellaneous tips & tricks
You now have the basics of downloading and managing references in Zotero! There are many other
neat functions available in Zotero, and the best way to learn is to start exploring the program. The
Zotero documentation and forums are also great places to start looking for tips and tricks. I also
recommend familiarizing yourself with what’s new in Zotero 7. Here are a few functions/options that I
find particularly useful:
Various ways to add references to Zotero
1) Drag and Drop: If you drag and drop a PDF into Zotero, it will attempt to find the correct
metadata and create a reference for it.
2) Find Full Text: If you only have a reference, you can right-click in and select “Find Full Text”.
Zotero will scour the internet for matching PDF files (these will most likely have to be open
access).
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3) Magic Wand: Perhaps you have a DOI for an article but don’t have a PDF. You can click the
magic wand tool at the top of the main Zotero window, and paste a DOI or other type of
identifier into it. If Zotero can find a matching record online, it will create a new reference in the
library.
If you happen to acquire the relevant PDF at a later date:
a) Put the PDF in the “Downloads” folder on your computer (or whichever folder you selected
as the Source Folder for Attaching New Files in ZotMoov settings in Part 3).
b) Go to Zotero and right-click on the reference.
c) Select “ZotMoov: Attach New File”.
d) ZotMoov will grab the PDF, move it to your syncing folder, and associate the reference with
it in Zotero, just as if you had clicked the Zotero Connector button in your browser.
4) Import: If you have bibliographic data stored in BibTex or other standardized formats, Zotero
can import it. From the top menu, click File → Import, and follow the instructions:
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Showing Items in Subcollections (a.k.a. recursive folders)
If you’re like me and you like it so that selecting a Collection shows all the references in that Collection
and its Subcollections then you need to enable this in Zotero. This behavior (also known as “recursive
folders”), is the default in Mendeley, but not in Zotero. However, it can be easily enabled by going to
the top menu and clicking View → Show Items from Subcollections.
Searching the Library
There are many ways of searching your Zotero library. It’s worth reading through the search
documentation to get a sense of what’s possible. Just note that you can adjust the way you search by
clicking on the little magnifying glass and selecting an option from the drop down:
Deleting PubMed entries
Some journals, such as Science automatically download a PubMed metadata attachment to the
reference. This can be annoying because it will seem like the reference has a PDF attached, when in fact
it’s just the PubMed entry.
I suggest creating a saved search which will identify any references with a PubMed attachment. Once
it’s set up, simply check the search once in a while, and delete the PubMed entries. Here are
instructions.
RSS Feeds
If you sign up for table of contents alerts from your favorite journals, you might consider sending them
straight to Zotero via an RSS feed. Here is how to do it.
Groups
Groups are incredibly useful when working with collaborators. A couple of notes about groups:
• Each of your group libraries is distinct from each other and from your personal library
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• You can easily drag references from one group to the other
• If you followed the setup in this tutorial, your personal library PDFs will be stored and synced
in your cloud service. However, your group PDFs will be synced on Zotero’s cloud, which
gives you 300 MB for free, with larger storage plans for an annual fee.
Happy Researching!
If you have any comments, suggestions or corrections, feel free to message me or drop a comment on
ResearchGate.