PDF workflows with DT in macOS

Most information I produce is in the form of text documents, but most reference information comes in pdf files. As DT is an information manager, I think it would make sense to discuss here ways to improve workflows with pdfs in DT.

In my case, although I liked Skim I ended up discarding it in order to work with DT. I don’t find of much use to tag the long .skim file which goes with a book in pdf format.

The reason I use DT’s pdf editor to annotate pdfs is because I use the Annotation Pane script. I am particularly found of it because it extracts the selected text from each pdf annotation and inserts it in a separate rtf file with a link to the pdf page it originated from.

I open pdfs externally with Apple’s Preview for a quick read or review without annotating, because it has a nice side panel that shows the outline of contents and my annotations. Skim is just not practical for this sole purpose because it requires to convert annotations each time. DT’s own basic pdf editor has no side panel.

If Skim’s pdfd format or any other app stored instead of one file for all annotations, one for each of them, making it possible to tag them separately, and keep them all synced to their pdf, I would rush to get it. Or if DevonThink was capable of rendering pdf annotations as if they were separate files, as CAQDAS apps do. Without this, I think the annotation changes that should happen after a second reading are just too troublesome -so here is a case of technology impairing what human information processing requires.

Would someone care to suggest ways to overcome some of the impediments I’ve mentioned here and improve the MacOS workflow described? It might be a good reference for other DT users as well.

I have been thinking about this problem too. Here is how I deal with a second review of documents where the annotations were generated with the Annotation Pane script:

  • I have the group folder open that contains all the documents annotations.
  • I have that folder sorted by URL, so that the annotations are sorted by page number.
  • Looking at the URL field I can see the page number and if there are already any annotations for a page, although inevitably I have highlighted the passage in the original passage in the pdf at the same time as making the annotation, so I will already know this. (The nice thing about how DT compresses short column views is that the page number is always visible at the end of the URL no matter how much the field is compressed)

I have experimented with a hot key which just brings up a folder with the annotations for the current page but I haven’t really had enough use out of it to refine it. If there is interest in the idea, I might still.


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Any image might be useful to show how you can keep the ‘private folder’ (reached by clicking the URL field of the document) with the annotations to the document side by side with the pdf being annotated

Quotations and documents side by side.jpg

This ‘private folder’ makes it easy to see what pages have already been annotated and any additional annotations added with the Annotation Pane show up automatically in the folder, sorted by page. I find this useful for a second or third review of documents when I want to remove superfluous annotations, add further annotations or supplement existing annotations with more detail or links to other documents. It also makes it very easy to select all the annotations to a document and use the Document Review pane script, to review the annotations’ metadata and update the spotlight comment summary.

(Sorry i cant pull of those neat little animated screenshots korm does !)


(just to be clear this only works if you generate your annotations using the Annotation Pane script. This is because the Annotation pane script keeps replicants of all annotations to a document in a ‘private’ folder linked to the document, irrespective of what folder you may put the annotation itself in. This is useful because you can move your annotations around in the folder structure, such as when you are developing an outline without breaking the relationship between the document and its annotations. If you use DT’s built in annotation template which keeps all annotations in a single file or Highlights, as korm describes in the post above this, which requires you to export your annotations into a folder in DT, you will have to manage these relationships yourself)

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That photo shows what I think is the most that can be achieved within DT at this stage. Congratulations for such a well thought setup within the limited means of DT in this respect.

I will follow Frederiko’s recommendation to order the rtfs by their url page, as it shows in that neat image. Also to click in the url field - I was clicking in the links in the body of the annotations -which open the pdf in the same window as the annotation!!

But I use Annotation Pane for a different purpose. I need to keep extracted annotation separated from my commentaries because otherwise I have no way to know what my writing amounts to. I’m concerned about the accesibility to other apps and the future development of Spotlight comments, so I’ve decided to separate my own writing from the quoted annotations in separate rtf files.

If DT comes up with an Scrivener-like contiguous view of rtf files, it could be used to display annotations in a view in which it would be possible to comfortably scroll the contents of all annotations. The stream is not synced to the page viewed in the pdf, but when one piece/file of the stream is clicked (or the link in its body inserted by Annotation Pane), the original pdf context of the annotation will appear. I think this is a better solution than the aforementioned dynamic display without clicking. To give an idea of how this could look, I attach an image.

Annotation Pane links each annotation to the pdf page it is extracted from, not to the exact location within the pdf page. This is no good for coding, but perfectly alright for annotating whilst reading books, journals, etc.

Clicking rtf annotations created by Annotation Pane directs to the pdf page. Not the other way around. I manually highlight each section of the pdf I extract a rtf annotation from with Annotation Pane. If and when DT’s pdf editor comes with a side panel for pdf highlights, if its contents are editable as they are in Skim and other pdf editors, and with the added functionality to make DT hyperlinks clickable there, it might be possible for Annotation Pane to include there a DT hyperlink to the rtf annotation it creates. In this way, clicking one of the highlights in such side panel would direct to its rtf annotation inside DT.

So I am sorry (partly) to say that in this respect it is on DT’s side to evolve in order to make the best of the very good functionality Annotation Pane is targeting at! And I hope it does so, because there are people who turn to CAQDAS apps just for literature reviews and reading, as one can infer from the tutorials available online for such usage. I know this the hard way because I was one of them, first with Atlas.ti and after with Maxqda. Experience tells me that these apps are good for coding accurately many short sentences with a defined set of tags that can be remembered. And they excel at target search and analysis of combinations of the used tags. However, they lack the freer possibility to search at once file names, content and metadata; to perform on the results reading and writing related tasks, not just tagging/coding and analysis of codes; and to have the files available to external apps. DT already provides all of these. Therefore, no competition from costly CAQDAS apps because of the different feature set for different purposes (coding / annotating). And no competition from PDF editors, because they do not provide the information management functionality to rearrange each single pdf annotation via tags, search and DT’s “ai” features.

DT can achive this just by improving its very basic pdf editor with a side panel for annotations (with clickable DT hyperlinks) and the much requested Scrivener-like view of several files. As I see it, Annotation Pane can put both to an innovative and good use.

I attach an image which shows the DT hyperlinks used when I annotate pdfs. I follow korm’s term differentiation among annotation with quote (automatically extracted by Annotation Pane to an rtf), and commentary on quote (my own writing, in another linked rtf).

Continuous lines represent that the url of the file pointed to by the arrow is in the url field of the pointing file. Only one url can be placed in the field, going from commentary to annotation to pdf.

Discontinuous lines represent that DT hyperlinks of the file pointed to by the arrow are inserted in the body of the pointing rtf. In this way, annotations which have been commented easily show if they have one or several commentaries.

The red discontinuous lines don’t exist in my workflow. They represent what I hope can be implemented in the future: clickable DT hyperlinks of corresponding rtf annotations inserted in the editable body of each pdf highlight.

I copy all tags from an annotation to its commentary. I can locate my comments and annotations to a pdf together because I tag both with a unique citation ID. And differentiate among them because my own writing is always additionally tagged with my name.

What I wonder is if I should use Annotation Pane for my commentaries on rtf annotations, since it would mostly be creating a folder for each single annotation I comment.

My workflow involves a lot of quick highlighting, often of pdfs that cannot be OCRed (blurry photos, too big after conversion etc.). Is there any way I can turn off the automatic popping up of the Annotation Pane when using tools like the “rectangle”? When I just need to make a note of an important spot, the Annotation Pane just slows everything down (having to close it every time).

Thanks for suggestions. Adam


I don’t really know. You may ask in the posting in the forum for the script, Annotation Pane.

Some confusion here. The annotation pane adam is referring to, is the pane which pops up when you use the annotation toolbar to inserts annotations like lines, rectangles and so on.

My solution is to rarely use the toolbar. I have the tools I use the most on the annotation toolbar linked to keyboard shortcut:
Line: Cmd-Opt L
Text: Cmd-Opt N (for Note)
Text Selection: Cmd-Opt T

Because my hands dont leave the keyboard, its then much easier to use Cmd W to close the pane which opens when you use these tools.