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Zotero Windows Setup

Zotero is a reference manager for Windows, MacOS and Linux.

Note: These instructions should work for Linux and Mac too.

I have also created a tutorial on how to use some aspects of Zotero that can be accessed here.

This blog post has some more detail about different ways to set up attachment syncing. I have personally found WebDAV to be more reliable overall (despite the occasional downtime of pCloud's WebDAV service).

Default Zotero Preferences I Change

  • Don't download website snapshots to save a lot space
    • Under edit, then preferences select the general tab
    • In the "file handling" section uncheck the "automatically take snapshots when creating items from web pages"
  • Don't share the child notes, links and tags with shared libraries
    • Under edit, then preferences select the general tab
    • In the "Groups" section uncheck the "child notes", "tags" and "child links" options
  • Change the default citation style to ASA 6th edition
    • Under edit, then preferences select the cite tab
    • In the styles section find the "American Sociological Association 6th Edition"
    • If this option is missing you can download the CSL file from here
  • Sometimes I like to see all of the citations within a folder and all subfolders, the show items from subcollections setting allows for this.
    • Under View select "Show Items from Subcollections"

Main Screen Columns

  • I prefer to have the columns organized in the following order:
    • Creator
    • Year
    • Attachments
    • Title
    • Extra

Zotero Add-ons

  • To install a plugin do the following:
    1. Select "Tools"
    2. Select "Add-ons", then click on the gear in the upper right
    3. Select "Install Add-on From File"
    4. Browse to the downloaded .xpi file
    5. Select "Open"
    6. Restart Zotero
  • Better BibTeX
    • I use this because I write mostly in markdown with pandoc and citeproc, Zotero's default exporting format sometimes causes issues with cite keys. Better BibTeX solves that issue. It can also auto update citation files. Below are the instructions for installation and configuration:
      1. After the restart I selected these options in the dialogue box: "Use the BBT default citekey format"
      2. I then deselect the "Enable drag-and-drop citations"
      3. I don't change anything on the next screen
      4. You will need to restart Zotero again
      5. Better BibTeX will then create a new key for all of the citations in your library
      6. When exporting select better BibTeX and that should help with citations using BibTeX or BibLaTeX
    • You download the .xpi file for installation here:

Zotero Plugins to Evaluate

  • There are many other plugins that I would like to try out or at least evaluate to see if they would be worth including into my regular plugins
    • A list that someone else uses - it looks like a good list
      • Actions & Tags - looks like lots of customizations for tags and other keyboard actions and such
      • Better BibTeX - Already use this
      • Better Notes - lots of zotero notes analyses and exporting functions
      • Bionic - adds bionic reading to pdfs (bolds the first couple letters of each word makes it easier to read)
      • sciPDF * Reference not sure what this is
      • Style - maybe this repo?
      • Tara - "Tara is a Zotero add-on for backup and restore preferences, add-ons, translators, styles. You can keep the same settings between different Zotero or restore history settings from the backup."
      • Translate - "Translate PDF, EPub, webpage, metadata, annotations, notes to the target language. Support 20+ translate services."
      • Zoplicate - "A plugin that does one thing only: Detect and manage duplicate items in Zotero."
      • Zotero OCR - "Zotero Plugin for OCR"
      • zotero-inspire - "Zotero plugin, fetching publication metadata and cite counts (w/ and w/o self citations) from the INSPIRE-HEP database (and CrossRef cite counts for papers in other fields)"
      • ZoTTS - "A Zotero plugin adding text to speech (TTS) functionality to various screens"
      • Zutilo Utility for Zotero - "Zotero plugin providing some additional editing features" - Note that it doesn't appear to be updated very often anymore and maintainer has stated they don't have much time for it anymore
      • Chartero - "Chart in Zotero"

Old Zotero Plugins

  • Not updated since 2022-04-04 - Zotero Citation Counts
    • To configure I do the following:
      1. Select "Tools"
      2. Select "Citation Counts Manager Preferences..."
      3. Under the "Get citation counts for the new items"
        1. Select "Semantic Scholar citation counts"
      4. Select "Tools"
      5. Mouse over "Get citation counts for the new items"
        1. Select "Semantic Scholar citation counts"
    • To use:
      1. Right click on any item in the main window
      2. Mouse over "Manage Citation Counts"
        1. Select "Get Semantic Scholar citation counts"
  • Not updated very often - Zutilo - "Zotero plugin providing some additional editing features"
  • Depreciated as of 2024-10-18 - Mdnotes

Links and Account Information

Note: It may not be a bad idea to configure all settings and Add-ons before you set up syncing

  1. To complete the instructions to install Zotero and setup the WebDAV file syncing, you will have to follow the instructions listed below:
    1. Download Zotero from the Zotero website
    2. Create a Zotero account here
    3. Create a pCloud account here
      • Alternatives to pCloud can be found here
  2. Setup WebDAV Syncing Instructions
    1. Download and install Zotero
    2. Select the edit menu and then select preferences
    3. Select the sync tab
    4. Sign into into your Zotero account
    5. In the file syncing section, select WebDAV in the dropdown menu
    6. Make sure https is selected
    7. In the text box add "webdav.pcloud.com:443"
    8. Enter your pCloud username (this should be your pCloud email account) and password
    9. Mostly to save space I also select "as needed" in the dropdown boxes that are labeled as "Downloaded files"
      • This makes it so that attachments will only be downloaded when you try to open the attached file rather than trying to download all of the file attachments for your entire library every time you sync.
    10. Press OK at the bottom of the settings dialogue box
    11. Click on the Green sync arrow in the upper right hand part of the Zotero window
      • Note for Windows: Syncing will fail on the first try that is normal (probably a bug) to fix this do the following:
        1. Select the edit menu and then the sync tab
        2. Reenter your pCloud password
        3. Press OK at the bottom of the dialogue box
        4. Click again on the green sync arrow
        5. Zotero should now sync correctly

Zotero Related External Applications and Integrations

  • Citation Picker for Zotero (for VSCode)
    • You must have Better BibTeX installed to use this
    • This allows you to use the same citation selector that you can use in MS Word or LibreOffice Word in VSCode
  • You can use Zotero in OnlyOffice by going to the "Plugins" tab and entering an API key
    • Make sure you save this API key somewhere you will not lose it, you will only be shown the API key once