Simple note taking question

Where do you recommend making notes about a document in DT?

In the past, I have used the Annotations box within the Annotations & Reminders section of the Inspector. But I do not like that this creates a separate ‘Annotation’ file within the db that is not directly linked to the document in question. It feels like this is the wrong place for me to make my notes.

I am an historian who uses DT to organize my archival documents. I would like to be able to make notes about a document while reading it that are both visible while viewing the document but also viewable outside of it i.e. in a list of notes (that are linked to the document). Thanks!

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I use a group containing the document and notes
I have a script that takes selected text and creates a note with a link back to the document


I would (and do this now) open a new document in a window along side the review document. I use the DEVONthink editors in Markdown, but any format works. Sometimes use ByWord on my Markdown documents. Or even use another external editor of choice, e,g. Word or Pages if you want text and images. Or a fancy text editor. Whatever. At the top of that document put the DEVONthink item link to the review document. Put that comment document in the same DEVONthink Group as the review document.


This needs more definition. There is no singular document in DEVONthink and the possibilities vary based on format. For example, if you’re referring to an image, Finder comments, custom metadata (in Pro/Server) or an annotation file would be the option. A PDF allows annotations in the file.

Thanks, Jim. These are ‘PDF + Text’ files which were originally image files that I ran through the ‘OCR to searchable PDF’ function.

Have you considered using Note annotations in the PDF?

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Hi. Are you referring to adding a ‘Note’ within the PDF or adding a ‘Text’ box?

For PDFs I like - you can export your annotations to markdown and then link them accordingly to the PDF in DevonThink.

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I just add notes into the pdf itself with text boxes. You can colour text boxes so they stand out, and I usually stick them next to highlighted text. When I’ve finished, I use the “summarise annotations” option to compile them in a markdown doc, which I keep with the paper. Usually I will add more thoughts into the markdown doc when I check it after.

I am mostly mimicking what I did on paper though - I never wrote notes separately in a notebook while reading, I just annotated the printed paper and then compiled notes from my annotations. DT is saving me the job of compilation (which is great) but I still go through the annotations in the markdown file and add any new thoughts, clarify anything that lost context once it wasn’t next to its source, etc. I have a tag that identifies these documents as belonging to a paper, and I have a naming convention so that they are easily identifiable.

Edited to add: sorry, I wasn’t very clear the beginning there: I read PDFs in DTTG, but the process works in DT Pro as well.


Hi. I am a historian as well. Here is what I do.

  1. I take notes separately in a simple text file saved into my “zettelkasten” group, often opening the file in BBEdit (my favorite text file editor).

  2. I take them separately by hand with a pencil and paper (when visiting the archives, pens are not allowed), scanning them as a PDF and adding that to my “zettelkasten” folder.

  3. I annotate the PDF document on the iPad using an Apple Pencil and GoodNotes—many archival materials are online now, making this pretty easy to do.

My favorite is 2), but due to time constraints (the need to go pretty quickly from reading to publication / presentation), I have been going back and forth between 1) and 2) this year. I haven’t been doing 3) so much.

I suppose I could type notes directly into a PDF (see some of the suggestions by others in this thread), but I have never found this to be worth the time or effort.

I have an article about this. Maybe this will be of some use. I was supposed to follow up on it with another article, but… a few years and a pandemic later, I haven’t gotten back to it yet :slight_smile:

Organization (the topic of that next article) is a thorny issue, but basically I am lazy and prefer to have everything in my “zettelkasten,” linking items from the text files to the relevant sources (or other related notes / materials) in other groups within the database. DT makes it easy to link to another file by just pasting the name of it into a text file.


I created a user defined meta data field called “short note”, where I jot down really short comments about a document of whatever kind. This is my go to when I just want to leave short remarks for later (“use this as starting point for project XY”) or short reminders (“seems illogical – check again”).

For deeper work with a given text, I sometimes write into the document itself. In RTF-texts I use a special formatting (blue, tiny font, indented) to characterize my own thoughts, in PDFs I use the tools that are provided.

And sometimes, it seems appropriate to use the Annotations-feature as intended.


I personally use Margin Note 3 when working on my philosophical documents. You can have your pdf, take notes, having both on the same screen; but also having your notes apart.

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Two observations:

  1. If you choose “copy item link” and then paste it at the top of the annotation in the annotation pane in the inspector, it is now linked to the original note.
  2. If you don’t like the separate annotations, you can always delete them. The annotation in the pane remains.
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Can you clarify what you mean by this?

The annotation “in the pane” is the one to the right of the document:

It remains even if the separate item in the Annotations group is deleted. I thought it might disappear.

This should only be true if you haven’t emptied the databases’s Trash.
If you are indeed seeing this after emptying the Trash, it’s a bug not a feature.

I would use Margin note 3 for anything other than a quick few words comment.
Probably best to use a purpose designed app such as MN3 if you are going to go back to your notes and compare info with items you have thought important from other papers.

Liquidtext is another such app, but subscriptions put me off

Just out of interest why don’t you just use the DEVONthink 3 note functions? What do you see as the limitations compared to Margin Note 3 and so on. I used to use Ulysses which is quite good but I didn’t find I really needed it when I have the search and AI capacities of DEVONthink 3 at hand.

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For PDFs I often use skim App to take notes inside the PDF file, you can even annotate highlighted parts of the document. These annotations can be exported, as Markdown file f.i.
As all the PDFs live inside DTP3 I have best of both worlds.

All of this is actually possible in DEVONthink too, see e.g. Tools > Document > Annotations and Tools > Summarize Highlights > as Markdown.