Help with Idiot’s attempt to develop efficient .pdf workflow for research

I know that “it is a bad workman that always blames his tools.”

So I won’t do that.

And my tools are pretty good I think - 12.9” iPad Pro, DEVONthink 3, DEVONthink to Go, GoodNotes and Adobe.

I need help with what should be a simple workflow to use in connection with my thesis research for a Masters that begins in September.

Here’s what I need to be able to efficiently do …

  1. After locating a relevant article on the web, I want to save it to DT and then either immediately or later (when I have time) proceed to read and annotate it (using Adobe currently - but open to suggestions if there’s a more efficient product), with the resulting annotated copy replacing the clean copy that was originally saved to DT.

  2. I’d like to be able to do this entirely from my iPad.

Sounds simple, right?

But I am really struggling with how to manage the relation between DTTG and Adobe. For instance:

  • when I finish annotating in Adobe using its Comment tools I want the result to be reflected in DTTG instead of the original clean version. Annotations are not’ automatically reflected in DTTG so I try to send the annotated version to DT via the Share icon in Adobe … but that takes me to Adobe’s interface to send the annotated version via email - which would mean a lot of additional steps to achieve objective.

I am more than sure that others have solved this workflow and are efficiently reading, commenting and saving their research assets in DT.

Do I need to do all of my annotating with the native DT3 pdf editor? I don’t really want to do that as Adobe’s is more feature rich.

Do I need to do all of my .pdf annotating outside of DT … and then save to DT only after all annotating has been completed?

How do I ensure that ongoing revisions to a .pdf saved in DT are reflected in DT?

I’m totally confused and frustrated - but I AM NOT BLAMING MY TOOLS.

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Sorry for your frustration but there’s actually no friction here.

Using the Document Provider in Acrobat, e.g., the part that looks like’s browser, you can access PDFs in DEVONthink To Go. After you close the document in Acrobat, the changes are reflected in DEVONthink To Go.

Why aren’t you just annotating in DEVONthink To Go?

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Thanks Jim. I was expecting an easy solve and you’ve suggested one. I was not aware of the direct access to Devonthink files from the Adobe app.

I’ll try the Dttg editor again as you suggest - I recall it being less flexible than the Adobe equivalent but perhaps I’m misremembering.

Thanks very much.

You’re welcome.
I personally prefer the framework we use in DEVONthink To Go versus mobile Acrobat’s tools. That’s just my comfort level though.

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The fully featured ‘pro’ apps always look better and seem to offer more shiny options.

But in truth, marking up a PDF for study purposes doesn’t need many bells and whistles. I annotate all my PDFs in DT2G (I am an academic in the Humanities and so burn through quite a lot of it!), using a variety of coloured pens, and highlighters. Every now and then, an arrow or a typed text box. I can’t think what else I would need. Your mileage may vary depending on your discipline (e.g. maybe you are a mathematician and need to enter equations or something…). But DT2G’s annotation tool set is simple and exactly what you need.

Jim’s work around through the ‘Files’ app works, of course, but keeping things in house in DT2G is just more efficient.

I do occasionally need to use Acrobat exclusively (some publishers insist on it for marking up proofs), but in that case I always use the Macbook Pro anyway.

Good luck with your MA thesis!


Appreciate your thoughts. For the life of me I haven’t found a way to draw a straight highlight across a line of text in the dttg editor. My tremors are perhaps the problem but what do you do to keep things tidy?

The text highlighting tool acts on selected text. Freeform highlighter does not. You’re just drawing at that point. There’s also a straight line tool.

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Any time :slight_smile:

Your highlighting should be straight in any PDF editor really (not just DTTG) - you’re not actually drawing a line - as Jim says you’re selecting text and the app is colouring it. So do make sure you’re selecting the right tool (the highlighting one). If your highlighting is not straight (and assuming the text is!), it’s giving you a hint that the PDF editor isn’t treating your markups as standard annotations (which means they’re not cross-compatible with other apps, and you may not be able to extract those annotations from another app in future).

I agree with @SebMacV though - do you actually need all the bells and whistles that some PDF editors provide if you’re just reading papers (I’m a scientist and also reading a lot). I’ve been testing PDFExpert (I’m trying to fix a different issue) and I’ve ended up removing the menu for most things that offers because all I need to do is highlight, add text boxes and occasionally draw something. All the other menu options are just noise. DTTG’s PDF editor can handle all of that, as well as occasional handy extras like deleting pages, merging, etc.


I definitely miss the feature to bookmark pages in PDFs in DT2G. It would ease finding a specific page, passage or annotation in long texts or books.

Also a digest function would come very handsome in order to note own thoughts regarding a selected text in a separate but linked file, as space to write annotations is limited in PDFs. It also would make finding annotations easier.

Switching between the text-highlighting and text-underlining tool is currently a bit of a hassle: it takes too long for my taste. I‘d rather prefer two separate easily accessible tools for that.

To put it short: I really love what the designers and developers at devontechologies have put together in the last years. DT is literally the best software I have ever used and with each release & update it’s getting even better. I use it every day on MacBook & iPad and cannot imagine working without it. You guys just know how to build high quality software.

And I really would appreciate that quality if it comes to reading, annotating and note-taking. I think if devontechologies would start developing or integrating more capable PDF tools (even with handwriting recognition?) instead of the Apple Framework, DT would be even more a must have software for knowledge workers.
At least I’d be willing to pay for such an upgrade right away.

Thanks for the generous comments. They’re appreciated!

This is already available as Annotation files (and has been for some time).
Open the Info popover for the document and you’ll see the Annotation field where you can create an Annotation file (in Markdown at this time) or jump to the document’s Annotation file. Here, I’ve opened two windows on the iPad with the PDF and Annotation file side-by-side…

Thanks Bluefrog for pointing to the annotation feature. I missed that somehow. As I understand it, this is designed to keep pdf and annotation file side by side, copying and pasting linked quotes from one to the other. I will try this at home on the big monitor, on the road with the iPad I am loosing quite some reading space. I‘ll try that too but my eyes these days are not as sharp as they used to be.

Initially I had in mind pulling several annotation files out of one pdf, all linked to its source and possibly to own thoughts on the topic. Like Zettelkasten. But that might just be a matter of taste.

While trying out the annotation feature I noticed another thing: to highlight or underline text, I do not have to activate the edit mode! Selecting text offers some tools for that directly. I didn’t catch that one as well, but it makes life much easier.

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