Extracting highlights from PDFs

:sweat_smile: :sweat_smile: :sweat_smile: Sorry, I have no idea how their iPad apps are. I suppose they are really bad at designing good iPad apps…

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You should be aware, though, that MaxQDA uses a proprietary PDF handler (Foxit I think), not the native Mac handler, which means you can’t start annotating in another app then move into MaxQDA and keep your annotations. This and a lot of other UI quirks related to its cross-platform model have kept me from getting into it for all but the absolutely necessary QDA purposes, despite shelling out (from institutional funds, not my own pocket) for 12 and 18.

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Ah yes. That is a deal-breaker for me… though I’d already given up because of the lack of iOS support.

Aside: Highlights’ latest update on iOS is getting some love:


Does anyone use Marginnote to read papers? I once used it and found out that it was very useful to do in-depth reading and understand the structure of the paper (the mindmapping feature). And I think it is also really good for those who want to memorize some details (the flashcard feature).

But later I gave it up because I think this e-reader like others focuses on a single paper. I want softwares like MAXQDA to help me link different papers and different annotations (from a bird-eye view). But I noticed that Marginnote now seemed to support organization of “multi-book reading notes all in ONE map”. Haven’t testes it out yet.

Anyone has some thoughts on this software? Appreciate your input :wink:

MarginNote user, here. Haven’t used it as much I originally thought I would, but I very much appreciate the idea of MarginNote’s highlighting, annotation and export options. For a while I used to export notes from documents to iThoughts, which was useful at the time. My workflow at the moment is based on pushing notes from reading materials in Readdle Documents into a Zettlekasten inspired system in Drafts, but if/when I ever need to do anything more involved, MarginNote is my “go to” for that kind of work.

Also, hat tip to LiquidText. I prefer MarginNote, personally, but they have similar feature sets.


I use it every day, both in legal and academic capacities.

It does not seem to be as powerful as MaxQDA, but it is awesome for tying up together different paragraphs from distinct PDFs.

The macOS version is its main advantage over Liquid Text.

Sync is not stellar, but definitely workable. And macOS app sometimes feels a bit slow to my taste, but works ok most of the time. iPadOS flies…

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Thank @ldebritto @jsamlarose for your input. Never tried LiquidText before. Just headed over to its website and checked some video tutorials. It seems interesting and supports interlinking different papers. Awesome!

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I’m currently developing an app that’s meant to improve on such a workflow. The app (Keypoints) is a plain-text focussed note-taking & PDF annotation app for the Mac. It stores each PDF highlight annotation as a separate plaintext (MultiMarkdown) note. These notes are self-contained, i.e., they each contain all relevant info (e.g., the PDF file & annotation info as well as the citation info which can be fetched from your reference manager).

Having individual, self-contained plaintext notes is crucial IMO – not only for reasons of maximum portability & long-term stability. This also enables you to sort/filter and organize them (e.g. via tags, color labels or ratings), mix & arrange them with other notes from other PDFs (via structure/overview notes), and link them together (via drag & drop or autocompletion). This allows you to create a network of semantically rich and linked notes, and to build your very own knowledge database.

Unfortunately, the app isn’t yet available as a public (alpha/beta) release, but the latest status report in the forums has some more screenshots and a 1-minute screencast that shows it in action.


Incidentally this book on MaxQDA has just been released for free:


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That sounds really interesting. Please keep us updated.


IAnnotate will export as plain text. Liquid text will export into a word document, without the hexadecimal colour coding.

Since you appear to be doing this on the Mac rather than iOS, DEVONthink Pro does allow you to (1) to extract quotes/annotate from a PDF in individual notes, (2) add comments to the note, (3) add tags (codes) and (4) link back to page/place in the PDF where the extract is.

You can then collect notes from the same or different papers by tag.

For a while I was able to do this in DTTG as well, but I haven’t been able to do this in DTTG for some time and certainly not with edit in place.

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Thanks for your info. I’ll check it out!

FYI I came upon another Keypoints video from the developer:


Thanks! Looks interesting! Will keep an eye on it.

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It looks very promising.

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This app looks great. I’m using Highlights much the same way, but I like your approach to generating individual notes. Is there an option to have a single note per pdf? And is there a beta?

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The app is built on the principle of atomic notes as one of its core concepts. All of the app’s filter, visualisation, PDF and data model features build (and depend) on this. So there likely will be no native support for having a single note per PDF.

That said, I plan to offer options to combine individual notes. Dragging multiple notes into a text editor will already combine them. In addition, I envision that one can export all selected notes to a single file, or preview all selected notes together (e.g. via integration with Marked 2). This could also include transcluded notes. And finally, I’d love to present multiple selected notes together in the app’s editor – similar to Scrivener’s “Scrivenings mode”.

Unfortunately, there’s no publicly available test version yet. Please see my reply here.

Exporting multiple notes to a single file — and especially a kind of Scrivenings mode and/or Marked 2 integration like you describe — would be fantastic. Looking forward to the app!

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I think Highlights doesn’t perform too great with regards to it’s promises. Also, subscription models are a red flag for me. I own DT pro office but have nor figured out note export sorted by highlight color. This would be great for integration with tinderbox and further processing. Anyone have tips for that?

Does anybody use pdfpen pro? It seems to be able to select botes by color and then export them. Price is reasonably steep, though.