Zotero Version 6 Released

Just an FYI, since we’ve often discussed citation managers here. Zotero just released version 6, and there’s now an iOS app.

I’ll have to poke around a bit to see how things work, but this might get me back to Zotero from Bookends. I moved primarily because there wasn’t a good iPadOS solution before now (I thought Zotfile was a hassle).


Keep us posted as to what you think. I went back to Bookends because it was a bit more flexible but I don’t care for subscriptions so I’d be willing to reconsider.

Please try to write real post titles that will help others identify quickly what this is about.

Will do — and sorry about that!

I haven’t tried it yet either, but I’m in the same situation—using Bookends, could be tempted. Especially since it doesn’t look like a Java application anymore.

My two questions: where’s it save all these PDFs, and are the annotations saved “down” to the PDF file? If I can index the Zotero folder with DEVONthink, I may have a new procrastination project for next week…

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Yeah, I need to do some reading before I just start moving stuff.

On storage, at least, I’m guessing it’s as it’s always been: files can be stored on Zotero’s servers (which works well enough, but academics will exceed the free tier fast), or with any service that supports WebDAV.

I’ll have to investigate to see if I’m right….

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Mmm … it looks like linked files might be the way to go. If I’ve understood correctly, it would eliminate the need to worry about WebDAV, and I’ve got plenty of available space in both iCloud and Dropbox.

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Well boo and hiss:

I’ll have to experiment a bit. Linked files might actually still be the way to go, with the understanding that I’ll need to access them with an app other than Zotero on the iPad.


This is interesting - I’m a keen Zotero user, as it’s cross platform. However, I’ve always used Resilo Sync to sync my files between computers. I wasn’t aware that I could sync via WebDAV, so I might look in to this.

Hmmm. Was following this to see your success. I’m intrigued by many aspects of zotero, in particular some of the close integration with Obsidian. But as I read and annotate my PDFs on an iPad, it is pretty critical that they can sync across platforms. Bookends perhaps still has the upper hand…

Just a heads up that the latest version of Zotero switches to a proprietary pdf highlight and annotation method. They did this to facilitate annotating of pdfs held in group libraries without fights among group users, or so they say. But I think it’s a terrible idea, because you’re reliant on Zotero working well to take your annotations with you, should you ever want to leave. Bookends, on the other hand, uses standard pdf annotations which you can edit on any other standard pdf app.


Source for confirmation? Didn’t see it in the linked article but might have just missed it. This is a pretty important issue for me.

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Having just ported over a bunch of bookends refs and PDFs I can confirm — none of my highlights recognized. Woah… definitely a deal breaker


I think I’ll stay with Bookends, subscription and all. :slightly_smiling_face:

I can’t replicate this.

All my files with highlights added via PDF Expert on the iPad have the highlights showing and are showing in Zotero.

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From the article (which has further details):

Why does Zotero store PDF annotations in its database instead of in the PDF file?

The new PDF reader in Zotero 6 makes PDF reading and annotation a first-class part of the Zotero experience.

To enable this tight integration, Zotero stores annotations in the Zotero database, not in the PDF file. This allows for fast, conflict-free syncing, including in groups, and enables advanced functionality that wouldn’t be possible otherwise.

Zotero 6 also offers various ways to export its PDFs with the annotations included in the PDF.

While I understand users desiring annotations being stored in the PDF, as an app developer I can fully sympathize with the decision for Zotero 6 to store annotations in the database. Storing them in the PDF severely limits your options to develop advanced features, and can make things like sync hard to impossible.

Having good sharing & (scriptable) export options to output PDFs with annotations included can help to satisfy the different needs.


Likewise and agreed. This is not enough to make me instantly drop Zotero, but it is something that I need to test out and keep an eye on. It seems that PDFs I annotated before this update using Preview have had their highlights retained in the new Zotero version. If they provide easy-to-use and officially supported export methods it is fine with me but it is definitely something to be wary of in this day and age.

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@Bmosbacker I would not describe Bookends as having a subscription. In my mind a subscription is a product that when you stop paying for it (monthly or annual) it stops working. On the other hand Bookends comes with 2 years of free updates. If, after 2 years, you no longer want to update (or want to update later on), that’s fine. The app will still work perfectly fine.

Overall I think I update my Bookends about every 4 years … until there’s enough changes in the app that I really wan the upgrade, or a huge Mac OS update has forced it.


Perhaps I have a different version? My version renews each year:

It looks like you bought via the App Store. I bought directly. I honestly didn’t even know they sold on App Store. I believe with that version there’s no choice for the developer: one time purchase or subscription. Here’s the page for purchasing directly and see the details. Before next Jan you can switch over:

I have no idea how much it is on App Store, but $60 for first time purchase, $40 for upgrade (which would be your case)