Zotero Version 6 Released

My mistake - total zotero neophyte :grinning:. The highlights are there, but not “extracted” to the note fields. I guess this has to be done manually or via zotfile, or something else? Clearly the comments above are referring to the annotations done within Zotero. I do worry about ease of getting annotations out.

Here’s what I ended up with:

Yes, a switch back to Zotero. Because the iOS version doesn’t play well with synced files, I still need to use Zotfile to automatically save PDFs to a folder in my iCloud Drive (Google Drive or Dropbox would work just as well). That puts the PDFs in a place that I can access from PDFExpert, no matter what device I’m on. I can still add notes to a source in Zotero, and those notes will sync just fine. (Thankfully this means I don’t need to use Zotfile for directly managing PDFs on the iPad, which was the part I always found fiddly and annoying.)

Using linked files + PDFExpert means I don’t get Zotero’s new annotation features, but the upside is that I get reliable sync without having to buy additional storage from Zotero. (Their prices aren’t unreasonable, but I already have +/- 25 GB in Dropbox thanks to referrals from the early days, and I’ve got 2 TB in iCloud. I might as well use what I have.)

If I need to extract annotations from a PDF, PDFExpert lets me export those to Markdown fairly easily.

@Bmosbacker and @Mathew_T_Mitchell, the Mac app for Bookends is a paid update about every two years if you want new features; what you already have keeps working. At least, that’s how it is for me. I bought directly from the developer. The subscription I’ve been paying for ($9.99/year, if memory serves) is for syncing between macOS and iOS.

Sorry, the source is that I asked Dan Stillman and that’s what he told me!


Interesting to see people’s reactions here.
I personally want my annotations to be in the pdf because I like them to be editable from different apps. I got burned by the demise of Sente and I have learnt my lesson. On the other hand, I’m in the minority maybe in that I couldn’t care less about the “advanced features” enabled by proprietary systems. Simple features, well implemented, are usually enough for me.

I’m also surprised to see such a pushback against Bookend’s modest subscription fee. I like to pay for the software I use, I don’t see why people’s labor shouldn’t be compensated. Even when I use open source software, like Zettlr, I send them $10 a month, which seems fair for an app I use every working day.


My sense is that, at least in this forum, there’s not an objection to subscriptions in the abstract, for the reasons you mention.

As a practical matter, though, there are limits to the number of subscriptions a person can reasonably maintain. The thread on annual subscription totals was an eye opener.

Sorry, yes, I believe the extraction of the notes from the PDF’s to the note field has always been a manual process, though from memory, Zotfile add on does automate that when importing in files that have been highlighted using it to sync between devices.

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I think this is exactly the point. I doubt anyone begrudges developers a proper return for their labor. The issue is the proliferation of subscriptions, which is in effect “renting” the application. Each individual has to decide what represents good and wise stewardship of his or her finances, including a reasonable budget for app subscriptions and/or purchases.

When deciding whether or not to pay a subscription I start by asking “do I NEED the features this app offers?” If I don’t NEED those features, though I may prefer them, I usually opt for the “good enough” non-subscription app. An example is an app like Carrot Weather. It is a great app., I like it but I don’t NEED the customizations. What I NEED is accurate weather data and forecast. The stock weather app provides that so I don’t pay a subscription for my weather app. Fantastical is another example. It is a beautiful app, the natural language parsing is, well, fantastic, and the feature set robust. But, I don’t NEED those features. I just need to add and see events on my calendar. I could add a host of other apps where I’ve made a similar assessment–Ulysses, TextExpander, perhaps 1Password (still reviewing), MindNode, and more.

As to Bookends, now that I realize there is a non-subscription version available directly from the developer I’ll probably go that route.



20 characters…

If you are interested in using the webdav syncing, there is an offer on stacksocial for 100GB of lifetime storage for $30 with Koofr. That should be more than sufficient for most PDF libraries, but there are also offers for 250gb and 1tb as well. Then you can configure Zotero using Koofr’s webdav setup. I’ve been using this setup for a few months and it’s been working well. Also I prefer the one-time payment without subscription.


That depends, though. There are apps where the updates only unlock new features (like Bookends). There are also apps where your data is accessible across multiple apps, so the subscription may come and go but your data is your data. I don’t dislike that model and I don’t see a problem with “renting” the app when I need it in that case. It’s like the app is an expensive power tool that you’re renting when you need to do a job (or, say, for your years of working professionally on X), but what you make with the tool is independent of the rental.
And then there are apps where everything about them is ephemeral (I assume that that’s what carrot weather is like). It may be harder to wrap one’s head around a subscription in those cases.

So yeah – lots of nuance to consider.

I had a look at the thread linked by @acavender about subscription totals. I think I don’t go anywhere near those amounts, primarily because I really only pay for a handful of things at this point: Bookends, Highlights (which of course is relevant to this thread because it does automatic extraction of standard PDF annotations…), Zettlr (via Patreon) and Taio. Hardly a huge sum. And none of those apps locks me into anything (in the case of Bookends, the synced .bib file is de facto an automatic export that you can open in BibDesk and other apps, and the PDFs, unlike Zotero are annotated in standard form so you don’t need any special export operation to be in control of your annotations…).

Here in New York City, a bitter, salty espresso comes easily to $3.50. It tastes nothing like the real thing (I’m from Italy…) and it’s gone in a minute. It’s hard not to feel hypocritical complaining about $10/month, say, for an app I work with 5hr/day when I’m sipping the aforementioned disappointing beverage for $3.50…

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Zotero still looks like a Windows 98 app - bad font & typographical spacing, no interface with Mac standard right-click etc. If they could port the iOS version back to the Mac with Swift UI, they might be getting somewhere.


Gotcha. Yeah, I guess I find my current Bookends workflow is still far more attractive (and as @dfay points out here, zotero is literally not that attractive), although I do love the zotero web clipper. reading the Obsidian discord channel, it sounds like this new version has caused some real frustration to some workflows.

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That’s correct. I’ve not used Zotfile for importing highlights recently, but it did work well. Most impressively it used the journal article page numbers from the database when importing which means highlight page numbers are correct, rather than starting at page 1. Zotero 6 itself relies on the PDF metadata being correct which it rarely is on older articles.

I pay for Zotero sync space in part because it works well with the iOS app, but also because it hopefully supports Zotero development (voluntary subscription!). The highlights sync well between the desktop and iOS and can be extracted as text or merged down into a PDF. I’ve not had any problem importing previously marked up PDFs.

I recommend Zotero to anyone looking for a reference manager. I wrote 100,000 words of dissertation with it. Though I’d recommend Bookends to anyone who is comfortable with AppleScript. The latter is much more powerful, but with a steeper learning curve. Zotero still is indispensable for me for its ability to scrape metadata from web sources but I only use it for that. Everything gets exported straight into Bookends.


I really like the new notes system. It offers some features one does not find in any other reference manager, only in QDA applications. Keyboard navigation is also quite good, despite not being a native app (it is better than Bookends in this regard).

Like @dfay here, however, I can’t get over the Win 98 appearance, with no dark mode support. I find that it looks like a toy for some reason. Also, the fact that one needs to install an additional plugin to edit the cite key seems kind of crazy considering that it is a reference manager. Perhaps version 7 will be the winner. Till then, I will just wait and see how it evolves.

BTW Bookends has a wonderful notes system in place. Plus, as of Jan 2022, the ability to export all annotations (self-created notes, or annotations within a PDF created by Bookends or another PDF app) at once. You select the group you want to work with. Exports in a way that it’s clear which article, and which page within article, is being referenced. A huge time saver for me.


Tangentially related, an article I stumbled across outlining use of Zotero beyond academic references (I dare say it would apply to [insert name of other similar application] also.)

I love organising my academic research in Zotero and have been pondering how I might use it more generally. That article is some inspiration. Being able to have multiple documents attached to a source (I sometimes add book reviews I find and third party summaries from the web) as well as notes is incredibly useful. The Zotero web capture tool is very powerful.

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I hadn’t considered using it for manuals and the like but that’s a good idea. I’ve given up on the Zotero web import, and instead save the webpages with SingleFile, in part because it causes lots of little files and one file is easier to sync.

I guess the only issue that might be is that the library is just a single library - but I guess they have collections which can help tame that.

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The Zotero browser extension uses the SingleFile library to save a webpage as a single HTML file. Works well. (It’s listed on the SingleFile github page).

Oh, I must have missed that change! In the past, it saved everything as lots of little files. For example, this site, saved in 2016. I’ll change the settings in Zotero now then to use this - saves doing things manually!

Have you been tempted to switch to Zotero 6 @ryanjamurphy ?