DEVONthink for BOTH the Research and the Summary Notes

This morning before church I’ve been summarizing a few research articles. After moving all of my research into DT and using DT exclusively for BOTH storing and creating summary notes of research articles, I’m finding that there is less friction and greater efficiency than when using two separate apps, e.g., storing research in DT but writing summary notes in Obsidian. Because DT handles so many different file formats, OCRs PDFs, and includes wiki style linking, tags, and more, I have one central repository for the research and summary of it. I typically have two DT windows opened side-by-side–the research and my summary notes.

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Once I’ve finished with my summary notes, I copy the note URL to my writing app for further use.

This is working well for me so I thought I’d pass it along–not as advocacy–but as information for anyone who may be interested.


I am interested in this workflow! After you have written your summary notes, you mentioned the copy note URL to your writing app.

In your writing app, are you now expanding on the summary note? Have you noticed a difference between using the writing app for the summary and your current structure.

I am always curious on finding a better flow for myself. I have yet to ‘find one’ that works for me. Some days, I find myself research in DT and then writing in Ulysses. Other times, I am researching, writing thoughts in Drafts, and then going to Ulysses. I have been tempted to go down the rabbit hole of Craft for writing again, I use Craft mainly for collaborative pieces.

I use Ulysses and DT for entirely separate purposes. DT is the repository for research and my summaries of it. I take the relevant summaries for a given writing project and insert them as material sheets in Ulysses for quick reference as I write; see the screenshot below as an example of communication that I’m working on this summer related to teen sadness, depression, and anxiety. Thus far, this has been efficient with little friction. Let me know if this is not specific enough; I’m happy to help.

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I do similar to what @Bmosbacker is suggesting. In my case I open the document in a separate DEVONthink window with the Annotations tab open in the sidebar. I create highlights, or annotations, or highlights with annotations, as needed. When I’m finished with this pass of the document, I close the window and use Tools > Summarize Highlights > as Markdown. This creates a separate markdown document beside the PDF, with all highlights and annotations (including annotations on highlights), in order with DEVONthink page links back to the relevant page of the document. I use that highlights summarization document to additional additional notes and for reviews later. Also, the highlights summarization document is a good starting point for using DEVONthink’s See Also & Classify to find suggested related documents and notes.

I was using the Highlights app on my Mac for this, and realized DEVONthink does the same as Highlights plus a lot more – so why use two apps when DEVONthink is better than the sum of two.

Thanks for posting your method @Bmosbacker


Thank YOU for posting–I did not realize that was possible. This will be a big help. I just wish the highlighting and annotation features were better in DTTG–I prefer using my iPad for reading, annotating …

Thanks again, I learned something valuable from your post.

I have not used DEVONthink to Go for years, but I don’t think I will start now. I prefer research, annotation, and writing on my MacBook because the process is never limited to a single document with the need to check a reference, or glance at a related document, etc. Even on a large iPad, that too much flipping and flopping around.

(Imagine how much better iPads would be if they had Alfred.)


I agree with you but I don’t like reading long articles on a vertical screen. It is more natural for me to have the iPad on my lap like a book and to use the Apple Pencil to annotate. :grin:

Thank you for the clarification!!! This sounds like a good blog post idea for expansion. One of the areas that I have yet to dabble in is the use of callback URLs. I know they should be helpful, just haven’t had the time to fully look into it and understand.

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I can understand that.

The beauty of the DEVONthink solution is that you can create the annotations using just about any software, and just use the Summarize Highlights feature in DEVONthink when you’re back on the ground with your macBook.

So, for example, if you have software you like to use on your iPad for annotation, and that software works with documents stored in iCloud or Dropbox (and others), then index those files in DEVONthink on the Mac.

Hope that’s not too complicated, but it works.

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That is intriguing. I’ll experiment with annotating a PDF with PDF Expert on the iPad, import to DT and see if the highlights can be extracted. If so, that will be awesome!

It seems, from the DT-Forum, that there might be some problems with the collaboration between DT and PDF-Expert. IIRC there are a couple of complaints, and there seems to be also no realistic solution within the next time.
I haven’t yet found any advantage of using PDF-Expert instead of DTTG or DT.

Just to be sure, you are aware, that you can open two instances of DT (and other Apps) side-by-side on the iPad?

I haven’t spent much time with annotating PDFs in DTTG–I’ll give it a try.

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I’m not sure if I’m promoting this too much, but you all might be interested in the approach I shared for this a couple of weeks ago:

The idea is to “stream” the annotations from your PDF reading into markdown notes. No button-pushing required. Annotate the PDFs in whatever app you want on whatever device you want. As long as they are synced to a DEVONthink database, this workflow will create reading summaries for you automatically.


It is a very nice approach, but the big issue for me, is mentioned already on your page. It is the requirement, to place the annotations in an order from top to bottom.
Sometimes a part of a text becomes more important for me, thru something I read later in that text. So sometimes I just go back then, and make a new annotation there.
Your script, as far as I understand, could not handle that situation, and therefore I am in danger, to “loose” some of my annotations.
Another wish I would had for an automatic approach would be an automatic link between the PDF, and the file with the annotations.
As far as I understood, this will also for the time being, not possible, with your approach, right?

Thanks, yes, it does work well.

I was experimenting yesterday with Zotero and Zotfile which does allow something similar to what Ulli wants to do.

In my case, however, it doesn’t quite work as the documents I mostly annotate are legal Cases and, for some reason, that particular type does not recognise the journal pagination and uses only the pdf pagination.

Generally this is true. There’s no easy way to see annotation creation/modified dates, so the script uses the order in which the annotations appear, front-to-back, as a stand-in.

This is actually trivial to do. However, it isn’t in the script linked above because I do it with a literature note that “rolls up” my reading session annotations, like this:

That note is in Obsidian. It is also the “annotation note” for the PDF in DEVONthink.

I’m not as technically proficient as many on this forum but I’m going to give this a try. Thanks!

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As you know @ryanjamurphy, I was quite excited about getting this set up. I’ve been using it now for a few weeks so some feedback if folks are wondering if it is worth setting up:

It is pretty great.

I love that I can mark up my PDFs (which live in Devonthink as an indexed Bookends folder) with whatever tool I want (on mac or ipad) and still have the annotations waiting for me both in Devonthink and Obsidian (as I’m having my annotations land in a folder in my Obsidian indexed folder in Devonthink). I also like that since there are links back to the Indexed devonthink pages, all my pencil scribbles are only 1-click away.

The only slight frustration is that Devonthink won’t always update synced files for me when I’m away from my machine. (I have a script to index my databases fairly frequently, but if my home machine goes to sleep :man_shrugging: ). But turns out, that’s usually fine, as I have such a backlog of annotations to work on that I rarely need to immediately work on those annotations immediately.


Hi Ryan - I’m having some hiccups with this, and wonder if you have too with DTPO updates? (I know it isn’t your responsibility to helpdesk this, but just curious if you have had to change the script at all).