+1 – exact same boat, have returned to MarginNote countless times to try to figure out a workable flow, always get completely confused by the syncing and non-interoperable annotations. Would love to just get a basic epub flow in Devon.
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ePub does not provide for annotations or bookmarks, afaict. At at least, I didn’t find any references to these terms in the ePub standard. So if a reader implements bookmarks or annotations, it probably does so on top of ePub. Which is inherently non-portable.
Also, it’s not really surprising that ePub does not allow for annotations/bookmarks: It is meant to distribute books, sometimes DRM protected ones. So, the underlying files should not be modified by an app.
I guess your best bet is to stay with the least bad reader you can find and use its bookmarks/annotations, risking that you can’t use them in another system.
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I’ve struggled with this for a long time–and have a lot of annotations stored in Kindle books that are essentially useless to me.
I read all my journal articles in PDF format, and then export the annotations from Zotero to DEVONthink in Markdown format (with links back to the original document).
Books I keep in Calibre, and read and annotate in the built-in reader app. I have Calibre keep annotation in the ePub document. When I am not at home (or on my Kindle Fire), I use the Calibre server feature to read the books in the web browser which syncs the annotations back to Calibre. When I am done with the book, I can export all the annotations from the Calibre reader app to DT in Markdown format (which again, links back to the original document).
Edited to add: And as @chrillek mentioned, I don’t think storing annotations in the ePub part of the standard–those ePubs when opened in Books, don’t show the annotations.
I don’t do this that often as simply I don’t need the annotations, usually. But that’s on me. When I need and want them, I simply look at them with the macOS Kindle App (which is pretty good) and usually export them to an email file that Amazon sends me. That file goes into DEVONthink Group for the “projects” associated with the annotations. SImple.
There might be an easy way to move away from eBooks without losing your annotations.
I’ve never used a Kindle, so not sure whether the My Clippings.txt file contains (all) Kindle annotations or what kinds of annotations Kindle offers at all.
If you used highlight annotations then this file should contain all of them (as far as I know) - and if you have a PDF version of the eBook then you could use Script: Add PDF highlight annotations from Kindle MyClippings to add your Kindle annotations to the PDF.
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Right, so when you have a garage full of specialty tools, like scripting, a robust syncing feature, and the most powerful organizational system, why would you park your car, err, ebooks in any other place? Implementing support for epubs would distinguish DEVONthink as the most powerful app when it comes to applied research, and it holds the greatest potential for addressing this two decades problem now with “non-interoperable annotations” via scripting so that annotations could then be imported into other apps.
EPUBs are here to stay, and their inadequacies or incompatibility at retaining annotations proves why apps like DEVONthink are necessary to make up for that. With Amazon changing the file type of its ebooks, it is also proving why it’s essential for those of us who enjoy reading ebooks to have an app like DEVONthink to show how powerful one’s library can be if we own our own digital material without being restricted in how we use them.
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I love car comparisons, being a bicycle rider.
Apart from that: I was only saying that there’s no standard for annotations of ePub. Which means that if you annotate them in one reader, you might run into problems with another reader. It doesn’t matter if one of these readers is DT, there simply is no standardized ways to highlight or annotate an ePub (nor any other HTML document).
In any case, I wouldn’t hold my breath waiting for DT to become an ePub reader (nor a Photoshop clone, nor something akin to Visual Studio Code nor an Excel alternative). The general approach seems to be to let specialized apps do what they can do best and have DT do what it can do best – not reinventing wheels. Neither those of cars nor of bicycles.
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Exactly, which is why the salient metaphor here wasn’t cars, but garages which here are the different apps supporting EPUBs. So since you’re a bicycle rider, if there are specialty tools to maintain your bike more efficiently and effectively so that your rides become better, why would you take your bike to a more inferior garage?
Why criticize my post by trying to make it seem that I’m enabling feature creep? I’m not changing the scope of DT in how it serves as an application, just requesting that it be inclusive to a specific file type in the same way that it serves support for PDF’s and Markdown and HTML and and other text based files.
Nothing’s being “reinvented” so not sure why you’d interpret my post to try to undermine something that is just a request to enable all of DTs current features onto EPUBs. It already does this with HTML files, with Markdown files, with PDFs.
All I’m asking is, so why not EPUBs?
I can’t speak for DT, but my answer to the question “why not enable annotations for ePub in DT?” would be: because all (or most, or a lot) of ePub Readers offer annotations in necessarily proprietary ways. If DT were to do the same, there’d almost certainly be users complaining why
- they can’t see the annotations applied with reader x in DT and/or
- they can’t see the annotations applied in DT in reader x.
Why would they open that Pandora box?
Annotations in PDF are apparently standardized, so a document can be annotated in app x and the annotations are available in app y. And even in this seemingly standardized situation things go awry, as posts here show.
Btw: bike repair shops (at least in Germany) are a bit like ePub readers: you have to find the least bad one. It’s nothing like with cars.
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Which is why scripting bridges the gap and takes much of the burden of “inter-operability” off of DT devs. I alluded to this earlier. At this point people who use EPUBs to read books already know what type of file format they’re using and aren’t likely to be asking for or blaming DT developers why “reader x” doesn’t have the annotations applied to EPUBs via DT. Also why would they be asking that if they’re reading it via DTTG?
The more you post these types of hypothetical situations, the more I’m seeing that you’re not wanting to be charitable at all for those of us who want to see a DT solution for EPUBs. Everything that an EPUB reader wants DT already has. It’s just the specific file type support that is being requested, which is based off of HTML which DT already supports.
Could you please post the URL to the Standard that defines EPUBs and annotations for EPUBS.
Usually, I have too many annotations and I get an error about the publisher only allowing a certain percentage to be exported…
Maybe I’ll try again…
I remember looking into this a while ago–but that was pre-DT and some new scripting skills–I’ll look at it again.
Google “ maximum export annotations kindle” to see maybe why.
Indeed, this is our stance on non-standardized and proprietary methods.
Additionally, if the developer of those methods changes something, we will be the ones with the support complaints and finger-pointing, and have to scramble to fix something they’ll likely iterate again.
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No one has said an unequivocal “No” to anything. However, DEVONthink is not DEVONthink To Go and the underlying frameworks are not all the same. If this happens in the future, it would be at a point where the same editor was running in our desktop and our mobile application. That is not Now. 
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NICE! Thank you!
(Sucks it’s Chrome only, but now I have a new project!)
OK thank you! I sincerely appreciate you dropping in and shedding some light on this.
You’re welcome