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Zotero 5.0.36: New PDF features, faster citing in large documents, and more

The latest version of Zotero introduces some major improvements for PDF-based workflows, a new citing mode that can greatly speed up the use of the word processor plugin in large documents, and various other improvements and bug fixes.

New PDF features

Improved PDF metadata retrieval

While the “Save to Zotero” button in the Zotero Connector is the best way to save high-quality metadata and associated PDFs to Zotero, Zotero’s “Retrieve Metadata for PDF” feature provides an alternative when you already have a PDF and want to quickly add it to your Zotero library as a citable item.

Traditionally, “Retrieve Metadata for PDF” has been a manual operation that relied on Google Scholar for some files, and long-time Zotero users know that trying to retrieve metadata for many PDFs at once could result in Google temporarily blocking access, causing the feature to stop working.

Zotero 5.0.36 introduces a completely new PDF recognizer, using a Zotero-designed web service that doesn’t rely on Google Scholar and that allows large numbers of PDFs to be recognized without rate limits. The Zotero client will send the first few pages of a PDF to the web service, which uses a variety of extraction algorithms and known metadata from CrossRef, paired with DOI and ISBN lookups from the client as before, to build a parent item for the PDF. The Zotero lookup service doesn’t require a Zotero account and doesn’t log any data about the content or results of searches. No data is now sent to Google Scholar.

Using this new service, Zotero will now automatically attempt to retrieve metadata for PDFs you add, whether that’s via drag-and-drop, “Link to File…”/”Store Copy of File…”, or clicking the “Save to Zotero” button on a PDF in the browser. (In a browser, we still recommend saving from the article page when possible.)

Automatic metadata retrieval after a PDF is dragged into Zotero

If you’re not happy with the results or want to add the parent item another way, you can right-click on the new parent item and select “Undo Retrieve Metadata”. There’s also a “Report Inaccurate Metadata” option to send the first few pages of the PDF and the retrieved metadata to Zotero developers for review.

You can disable automatic metadata retrieval in the General pane of the preferences.

Automatic renaming

When PDFs are added to existing Zotero items or metadata is retrieved for a PDF, Zotero will now automatically rename the file based on the parent metadata. This applies to both linked and stored files. A future version of Zotero will provide additional options for customizing the naming format.

You can disable automatic renaming from the General pane of the preferences. (Files saved along with items from web translators have always been automatically renamed and aren’t affected by this setting.)

Custom PDF viewer setting

Zotero opens PDFs using the system PDF viewer by default, but you can now choose a different PDF viewer to use for files from Zotero. This might come in handy if you’re happy with your system default for most PDFs but there’s a particular program you prefer to use for annotations (or if you’re just not sure how or are unable to change your system default).

'Open PDFs using' setting in the Zotero preferences

Faster citing in large documents

When you insert a citation into a document using Zotero’s word processor plugin, Zotero needs to scan the entire document for citations to ensure correct formatting. Citation style requirements such as ibid or name disambiguation mean that the format of a given citation may depend on the citations that precede it, and bibliographies depend on the presence of, and in some cases the order of, all citations in the document, including any that may have been deleted or moved around since a citation was last inserted.

In longer documents, scanning the entire document can take multiple seconds or even minutes, and these updates can become disruptive to the writing process. Common workarounds include splitting up long documents into chapters or using less-demanding citation styles during writing to increase the speed of citation inserts.

Zotero 5.0.36 adds the ability to disable automatic updates and defer citation updating until a manual refresh is triggered. With automatic updates disabled, citation inserts will remain instantaneous regardless of the size of the document.

To disable automatic updates, click the Document Preferences button in the word processor plugin and uncheck “Automatically Update Citations”:

Zotero Document Preferences window with Automatically Update Citations unchecked

To illustrate how citation inserting works with updates disabled, let’s look at an example. Say we’ve added a citation for a paper by Jessica Smith using APA style:

Citation for '(Smith, 2017)'

If we then insert a paper by James Smith, Zotero will create a citation in the default format required by the style without taking into account other citations in the document:

Citations for '(Smith, 2017)' and '(Smith, 2018)' with a dashed underline on the latter

Zotero adds a dashed underline below newly added citations to remind us that they haven’t been updated (though keep in mind that existing citations later in the document might also now be incorrect).

It also replaces the bibliography with a warning:

Automatic citation updates are disabled. To see the bibliography, click Refresh in the Zotero plugin.

We can quickly insert citations this way without waiting for each update. When we’re ready to submit our document, we click the Zotero plugin’s Refresh button:

Citations for '(Jessica Smith, 2017)' and '(James Smith, 2018)'

Zotero scanned the document and updated the citations and bibliography to conform to the style rules, which in this case require disambiguation for lead authors with the same last name.

To avoid accidentally submitting a paper with unformatted citations, we recommend leaving automatic updates enabled unless you find that inserts are taking too long for a given document.

Other changes

Zotero 5.0.36 includes a number of other improvements and bug fixes, including a cleaner user interface on Windows, lower idle CPU usage, and more. See the changelog for the complete list of changes.

Zotero 5.0 and Firefox: Frequently Asked Questions

In A Unified Zotero Experience, we explained the changes introduced in Zotero 5.0 that affect Zotero for Firefox users. See that post for a full explanation of the change, and read on for some additional answers.

What’s changing?

Zotero 5.0 is available only as a standalone program, and Zotero 4.0 for Firefox is being replaced by a Zotero Connector for Firefox that allows you to save to Zotero as you browse the web, similar to the Chrome and Safari extensions that have been available for years for use with Zotero Standalone.

Why is this happening?

Mozilla is discontinuing the powerful extension framework on which Zotero for Firefox is based in favor of a new, more limited extension framework, and it’s no longer technically possible to create a tool like Zotero for Firefox within the browser.

Will you change your minds?

See above.

Won’t this ruin everything that’s great about Zotero?

We don’t think so. Zotero has been available as standalone version since 2011, and many people have preferred it over the Firefox version — and we’re now able to focus on making it better for everyone, without making compromises to fit everything into a tiny pane or spending time keeping up with constant Firefox changes. The Zotero Connector still provides powerful browser integration and an unmatched ability to save as you browse the web.

In recent months, we’ve made numerous improvements to the Zotero Connector to bring it in line with Zotero for Firefox’s browsing-related features, and the Connector already offers some functionality that Zotero for Firefox never did, with more on the way. Since the Connector works in Firefox, Chrome, and Safari, you can use Zotero with whichever browser you prefer, or even multiple browsers at the same time.

OK, if I’m running Zotero for Firefox, what do I have to do?

First, install the Zotero Connector for Firefox from the download page, which will replace Zotero 4.0 for Firefox. Next, from the same page, install Zotero 5.0 for Mac, Windows, or Linux.

You can also install the Zotero Connector in any other browsers that you use.

If I already have the Zotero Connector for Firefox, what do I have to do?

Make sure you’ve also installed Zotero 5.0 from the download page, and leave it open while you browse the web so you can save directly to it.

If I’m running Zotero Standalone 4.0, what do I have to do?

You can upgrade to Zotero 5.0 via Help -> Check for Updates from within Zotero, or you can reinstall Zotero from the download page.

If you’re also running Zotero 4.0 for Firefox, you should first install the Zotero Connector from the download page and restart Firefox.

If you’re using the Zotero Connector for Chrome, you don’t have to do anything else.

If you’re using the Zotero Connector for Safari, check for updates from the Extensions pane — you should have 5.0.23 or later. You can reinstall the Connector from the download page if you have an older version and an update isn’t showing up.

Will I lose my data?

No. Zotero 5.0 will automatically detect and upgrade your existing data. If your Zotero data directory is located within your Firefox or Zotero profile directory, it will be automatically moved to a “Zotero” directory in your home directory, where it won’t be affected by refreshing or uninstalling Firefox.

Where did the Z button in the Firefox toolbar go? How can I open Zotero without it?

Instead of clicking a Z button in the Firefox toolbar, you now switch to Zotero as you would any other program. (See Switching Between Programs for tips on doing this efficiently. Short version: Use the dock/taskbar/launcher or Cmd-Tab/Alt-Tab. Don’t waste time minimizing or moving windows to access what’s behind.)

You can also arrange your windows so that Zotero is visible while you’re browsing.

What about the “Save to Zotero” button?

The button still exists in the browser toolbar, and, as before, it will show you an icon representing the data Zotero detected on the page: webpage, journal article, newspaper article, etc.

If you don’t see the icon, check your browser’s extensions pane to make sure you have the Zotero Connector installed. In some cases, the button may appear in the overflow panel accessible from the right edge of the toolbar.

How can I choose what collection to save to?

Just as in Zotero for Firefox, select the desired target collection in Zotero before clicking the save button. See Switching Between Programs for tips on accessing Zotero quickly.

An upcoming Zotero Connector version will provide the ability to choose the target collection from within the browser itself.

Are there any features that are no longer available?

While we’ve worked to make all browsing-related functionality available via the Zotero Connector, a few features either haven’t yet been migrated over or aren’t possible in the new Firefox extension framework.

Planned, but not yet available:

  • “Attach Snapshot of Current Page” (snapshots are still available when saving new items)
  • “Create Zotero Item and Note from Selection”/“Add Selection to Zotero Note”
  • “Save Link As Zotero Item”

No longer possible:

  • “Save to Zotero” option in the Firefox open/save dialog — workarounds: find the article page instead and use the “Save to Zotero” button to download the metadata and PDF automatically (recommended whenever possible); preview the PDF in Firefox and click the “Save to Zotero” button; drag the PDF link to Zotero; save the PDF to disk and drag into Zotero; add Zotero as PDF handler in Firefox and choose it from the open/save dialog (not currently possible, but planned)

What if I can’t install separate programs like Zotero at my institution?

Zotero can be installed without administrative privileges on most systems. You can also ask your IT department to install it for you.

It’s worth noting that the Firefox extension framework used by Zotero for Firefox for many years granted equivalent system access, so from a security standpoint there’s no difference between the previous Firefox extension and the standalone program. If anything, the standalone program is more secure, as the Zotero Connector code running within your browser is limited by Mozilla’s new WebExtension framework.

If you really can’t install separate programs, you can still use the Zotero Connector in your browser and save directly to your online library, but you’ll need to rely on the more limited web interface for managing your data. (Improvements to the web library are planned, but the desktop client will remain the recommended way of interacting with your Zotero data.)

What if I used multiple Firefox profiles to keep my Zotero data separate?

Zotero 5.0 supports the same profile system as Firefox. See Multiple Profiles for more info.

What if I’m using Zotero plugins that haven’t yet been updated for Zotero 5.0?

Most plugins have been updated, at least in beta form, so first check with the plugin author.

If a plugin you rely on hasn’t been updated, you can use the Zotero Connector for Firefox with Zotero Standalone 4.0, which is still available from the download page, for a while longer. Install the plugin from the Tools -> Add-ons -> Extensions pane in Zotero. Some Connector features may not work properly with Zotero 4.0, but you should still be able to save items to Zotero from the Connector.

How much longer can I use Zotero 4.0 for Firefox?

Zotero 4.0 for Firefox will cease to work in Firefox 57, which will be released on November 14, 2017, and existing Zotero for Firefox users will be upgraded to the Zotero Connector shortly before then. If you need to use Zotero 4.0 for Firefox for longer, you should switch to the Firefox 52 Extended Support Release, which will be supported by Mozilla until June 2018, and disable updates for the Zotero extension by clicking “More…” next to Zotero in the Firefox Add-ons pane. (Remember to re-enable updates when you later switch to the Zotero Connector.) If you’re already running the Zotero Connector, you can reinstall Zotero 4.0 for Firefox from the download page. Note that Zotero 4.0 syncing will cease to work in early 2018.

To benefit from the many improvements in Zotero 5.0, and to obtain support in the Zotero Forums, we recommend upgrading as soon as possible.

A Unified Zotero Experience

Since the introduction of Zotero Standalone in 2011, Zotero users have had two versions to choose from: the original Firefox extension, Zotero for Firefox, which provides deep integration into the Firefox user interface, and Zotero Standalone, which runs as a separate program and can be used with any browser.

Starting with the release of Zotero 5.0, Zotero for Firefox and Zotero Standalone have been replaced by a single standalone application for users of all browsers. A new Zotero Connector for Firefox, similar to the extensions available for Chrome and Safari, allows saving to the Zotero application or in a single click.

the Firefox toolbar on an Amazon webpage showing a book icon and a tooltip saying Save to Zotero (Amazon)
Saving to Zotero from the Zotero Connector for Firefox

If you’re using Zotero for Firefox, you’ll soon be upgraded to the new Zotero Connector for Firefox, which provides the same “Save to Zotero” button in the Firefox toolbar that you’re used to. You’ll then need to install the standalone Zotero application to access your data. Going forward, instead of clicking a “Z” button in the Firefox toolbar, you’ll open Zotero like any other program on your computer. The Zotero application offers the same interface and runs off the same database as Zotero for Firefox, so you’ll be able to pick up right where you left off.

If you’re already using Zotero Standalone, you can continue using Zotero as you were before — with some new features available in the Zotero Connector for your browser.

Why is this happening?

The reason for this change is technical, and, unfortunately, out of our control: Mozilla is discontinuing the powerful extension framework on which Zotero for Firefox is based in favor of WebExtensions, a new framework based on the Chrome extension model. WebExtensions offer many advantages, including improved browser performance, improved security, a fine-grained permissions model, and the ability to create a single extension that runs in both Chrome and Firefox (as we’ve done with the Zotero Connector). The trade-off is that it’s no longer possible to create an extension like Zotero for Firefox that affects the browser in more profound ways (adding an entirely new pane or tab, creating native-looking windows, adding options to the open/save dialog, etc.) or that uses low-level features of Firefox to manage a database, access the filesystem, or run local programs.

But while we’re not able to continue offering the full version of Zotero for Firefox, we think that this change will ultimately benefit the Zotero ecosystem going forward. The Zotero interface will no longer need to fit into a small browser pane, allowing for a much richer user experience. Offering a single version will mean that documentation and instruction can be greatly simplified. And most importantly, Zotero developers will be able to spend less time maintaining separate versions and responding to Firefox changes and more time improving Zotero for everyone.

In the lead-up to Zotero 5.0, we’ve worked hard to add features that were previously available only in Zotero for Firefox, such as institutional proxy support, to the existing Chrome and Safari connectors and the new Zotero Connector for Firefox. Those changes are documented in a separate post. As Mozilla and Chrome add additional capabilities to their extension frameworks, we’ll continue to add new features to the connectors.

When we launched Zotero a little over 10 years ago, the Firefox extension framework allowed us to create a new type of research tool that lived where people worked, in the browser itself. Today, we think we can offer the best of both worlds — unparalleled extensions for every browser, all connecting to a powerful standalone app. While it’s tough to say goodbye to the original version of Zotero, we couldn’t be more excited about Zotero’s future, beginning with Zotero 5.0. Here’s to the next 10 years.

Other questions? Check out the FAQ for additional details.

Zotero 5.0

We’re delighted to announce the release of Zotero 5.0, the next major version of Zotero and the biggest upgrade in Zotero’s history. Zotero 5.0 brings many new features, as well as a huge number of changes under the hood to improve Zotero’s responsiveness and stability and lay the groundwork for other big developments coming soon. We’ll be highlighting some of the new features in upcoming posts, but for now see the changelog for more details on all that’s new.

Download Zotero 5.0 now to get started with the new version.

If you’re already using Zotero Standalone 4.0, you’ll be offered the choice to upgrade soon, or you can update now via Help -> Check for Updates. (Windows users may wish to reinstall from the download page instead to rename the program from “Zotero Standalone” to “Zotero”.) Your database will be automatically upgraded to work with the new version.

If you’re using Zotero 4.0 for Firefox, be aware that Zotero 5.0 now runs only as a standalone application, and a new Zotero Connector for Firefox replaces the full Firefox extension. We’ve written a separate post explaining this change. Existing Zotero for Firefox users will soon be upgraded to Zotero Connector for Firefox and will need to install Zotero 5.0 to continue accessing their Zotero data locally. If you install Zotero 5.0 now, be sure to install the Zotero Connector for Firefox from the download page as well.

Thanks to everyone from the Zotero community who has helped test Zotero 5.0 over the last year and get it ready for today. We’re excited to finally share it with the world!

Indiana University Survey of Zotero Users

As part of a grant funded by the Alfred P. Sloan Foundation to analyze altmetrics and expand the Zotero API, our research partners at Indiana University are studying the readership of reference sources across a range of platforms. Cassidy Sugimoto and a team of researchers at IU have developed an anonymous, voluntary survey that seeks to analyze the bibliometrics of Zotero data. The survey includes questions regarding user behavior, discoverability, networking, the research process, open access, open source software, scholarly communication, and user privacy. It is a relatively short survey and your input is greatly appreciated. We will post a follow-up to the Zotero blog that analyzes the results of the survey. Follow this link to take the survey.