Making Progress on Annotation Limitations

I’m currently testing DT to see if it do what I need. I want to store all file types and comment on all file types. I’ve searched this forum for ways to do this and have noticed a lot of frustration over the current methods of annotation. Hopefully DT will improve the annotation functionality in the future. In the meantime, I’m almost convinced that I can get DT to work well enough for what I need by using the Data/New From Templates/Annotation script.

I’m basically convinced by Bill DeVille’s suggestions to use a RTF document for all annotations rather than try to embed them in original docs (not because I care to maintain pristine docs but because I’m worried that I’ll lose these in the future when some software does not support them correctly). Also RTF docs can be attached to all file types.

Two very valid complaints are made about the Data/New From Templates/Annotation script:

  1. If a URL is already inserted into the original document, the new Annotation link is not inserted into the link field.
  2. It is difficult to determine which files have annotations.

Here is a way I can see to resolve these issues. I’d be interested to know if others have better ideas!!

  1. If the original document already has a URL, go ahead and create the Annotations document (Data/New From Templates/Annotation script). (Or, if you already have an Annotations document or other document you want to use as the primary link to this original document, open it.)
  2. With the new Annotations document open, copy the link of that document (Edit/Copy Item Link)
  3. Go back to the original document, and choose Tools/Show Info.
  4. Paste the link into the URL field (if you ALSO want the URL that is already in that field, copy and paste that URL into the new Annotations document before step 2).
  5. Make the word “Annotated” the first word in the Spotlight Comments.

By doing this, you will have an easily accessible direct link to your annotations for any original document (if you have additional documents to link to the original document, you could insert those into your Annotations document)

Now, there are several ways to tell if you have an annotation:

  1. The blue ball icon and URL link at the top of the original document.
  2. The “quote or comment” icon that now appears by the name of the document (because you have a comment in the Spotlight Comments field, an icon will appear next to the name of the original document at least in list view. (I realize this is not as useful if you use the Spotlight Comments field for other reasons).
  3. You can see the word “Annotated” in the Spotlight Comments column if you manually include the Spotlight Comments as one of the columns to view when viewing your documents.

What I like about Bill DeVille’s methods (using an RTF document for annotations) is that I feel I have complete control over the annotations document. I realize other programs do annotations in a much more simple, elegant way, but I’m concerned about portability, future use, importing and exporting these annotations. I would however, be interested to know if anyone can recommend another program that does annotations better than DT and does them in a way where they are portable (You can easily transfer them to another program if you want, etc.).

I agree this method is a work around, and I do trust DT will improve in the future. Here I’ve summarized what a lot of people seem to be requesting:

  1. Have a visible indicator so users can easily see which documents have Annotations. (Also: be able to click on the visible indicator to directly open the Annotations.)

  2. Create a metafield (or some such) that only links to the Annotations document so it doesn’t have to share the field with other links.

  3. Let the user be able to choose to always have the Annotations open whenever the original document is open. It would be nice to be able to have a small view of the Annotations document open (to quickly make short notes) or to have a larger view of the Annotations document open so you can view both the original and the Annotations side by side (or in tabs or a separate pane, etc.)

  4. Have an option so when you copy part of a document the reference and a link to the exact place you are copying is also copied, so when you paste it, you have the original document reference, page number where you are copying from and can link back to that exact place you were quoting (and not just the entire page). (You can currently do some of this manually more or less with copying and searching and finding so it should be doable via a script.)

  5. Remove the “Type your note here.” text from the Annotation template, or at least select the text on creation, so that any typing will delete it and insert the new text.

  6. Be able to create other metadata fields for summaries or other info users want to attach to files.

Finally, I’m wondering if the field “Attached Script” in Show Info could be use to create a script that will automatically open the Annotations field every time a document is created?

Attached script
Script: This field allows you to attach an AppleScript script to any item in DEVONthink Pro Office, documents as well as groups. The script will be executed every time you view the item in a Split view or Three Panes view as well as when you open it in a separate document window. Click the Select button to choose the script to attach.

I am a COMPLETE newbie to DT (I haven’t even figured out the navigation yet), so I apologize if this is stuff everyone already knows. I’m just struggling to figure out if DT will work for me or if I should consider a different program instead. Thanks for any feedback!

I hadn’t thought of using an always-visible Spotlight Comments column as a reminder of annotations - good idea (not that I relish the thought of having to go and amend all my annotated docs, so may not actually use this!)

Great compilation of the various requests and issues regarding annotations. On request #4, ideally this could also be done by reading a document, highlighting relevant passages with Format>Highlight, then copy over all highlighted passages with references and links with a single command.

The more of these that are incorporated into future revisions of DT, the better.

I wonder if you could write an Applescript to quickly make the changes in Spotlight Comments to all your annotated documents?

I like your clarification to suggestion #4! I too look forward to improvements in DT.

(Thanks for replying, this is my first post, so it was nice to hear from someone!)

That’s true, a script might be possible though I don’t know how myself.

Great first post, see you around the boards.


These are solid recommendations. At the same time, I would call attention to the needfor improvements in the handling of PDF annotations. I have already submitted some ideas here:

Much as PDF annotations do have well-known limitations, some of which you address, they also have unparalleled strengths in terms of visualization, expressivity and overall usability (e.g. a simple graphic such as an arrow can be more eloquent than dozens of words).

I LOVE these suggestions. It is very useful to mark a pdf visually. I’m planning to do more of this, but I’ve been a bit hesitant because of reports that these annotations might disappear or get corrupted in some way. What has been your experience with this? I don’t want to spend a lot of time marking things just to have them disappear or get messed up!

In the course of several years of annotating, I have only had one accident that resulted in data loss. The culprit was OCR: The OCR engine of Adobe Acrobat is the only one I’ve found that does not discard annotations. As a corollary, I never scan pre-annotated PDFs with DevonThink. But this is no longer a problem for me, as I routinely OCR all my new PDFs before annotating them (and I do so with DevonThink, which provides a far superior engine).

Even this very minor risk can be addressed by ‘flattening’ the annotations before scanning. The ‘flattening’ prohibits further changes to (or deletions of) existing annotations but, on the other hand, your annotations are guaranteed for posterity. Again, to my knowledge, only Adobe Acrobat provides a way to flatten annotations.

I have not discovered any other risks and, to my experience, annotating PDFs is safe. Safer, in fact, than having a bunch of separate DevonThink text annotations which, while wonderfully searchable, also prone to deletion, since all it takes is an accidental depression of the “delete” key (and DevonThink unfortunately gives no warning before placing an item in the trash, whereby it may be lost forever).

All in all: I would invite the developers to consider improving the valuable PDF annotation scheme in DevonThink.

Re deletion in DEVONthink: It’s undoable (Command-Z) if that’s immediately invoked Absent the Undo command, the deleted item is sent to a DEVONthink Trash, and can be recovered from there. A deleted item isn’t really “gone” until one empties the DEVONthink Trash to the System Trash and empties the System Trash.


Thanks for the feedback on pfd annotations. I noticed text annotations are not searchable in DT so I may limit myself to highlighting passages and adding graphical arrows and such and then making notes in a separate annotations file.

Now I’m wondering if it might be better to do most annotating in Sente (or some such) and then transfer or index the results to DT. There is a lot of discussion of how to use these two products on the web, but they are mostly small snippets of information. I’d love to find one recent detailed instruction guide for using the two products together!


Thanks for your explanation!

It would be nice to have some feedback from DT when a file is being deleted, perhaps a special “this is being trashed” sound to alert you so you can quickly undo if you did it by mistake.

I agree that some (audio)visual feedback would be useful, as we all tend to empty our trash recklessly on occasion, without double-checking that no valuable items have been misplaced there. There is nothing wrong with the behavior of the Finder in that respect (audio feedback, and optionally a pop-up warning), which could therefore serve as a good model for DT, as well.

happyscholar, I am afraid I cannot help you re Sente/DT integration, as I am a longtime and avid user of Bookends. I have heard about the extraordinary note-taking capabilities in Sente but have never tried them out myself.

Well, I downloaded Sente today, but I’ve spent a frustrating hour trying to figure out how to export and/or copy the notes to another file. Despite much web searching, I can’t figure this out. It should be simple, but it appears you need another script to do it.

Do you make notes in Bookend and coordinate them with DT? How well does that work? If you’ve had some success, I might give it a try.

I’m surprised to hear about these difficulties with Sente—I was under the impression that it handles notes and annotations expertly. A major weakness of Bookends, in fact, is that it does not support Applescript. Nonetheless, the DT developers somehow pulled out a template-script combination which produces a new RTF note with the following information:
— Title of the reference selected in Bookends
— Author of the currently selected reference
— Year
— Keywords

Additional space for typing notes is provided by the template. Also, the URL of the note is set to the “bookends://” URL of the corresponding reference.

All in all, it works wonderfully.

If you are able to read Applescript, and also comfortable with creating custom bibliographic styles in Bookends, you will have no difficulties automatically importing any fields you want (e.g. notes).

Sente does have a nice way of handling annotations, but I can’t figure out how to cut and paste (or export) all the notes for one document. I thought it would be very easy, and I assume there is a way, but it is certainly not easy to figure out.

Thanks for the detailed information on Bookends. I will try that out!

For the benefit of anyone who finds some value in this thread, I did figure out how to copy notes from Sente into DT. It is not at all difficult, but also not at all intutive. Here are some instructions: … rint-notes

I am now thinking of the following workflow. I’ve tested this so I know it works, but I don’t have much experience yet as I’m just trying to figure this out.

  1. Import new file into DT. (Delete original.)

  2. Create a new annotations file (Data/New from Template) which is automatically linked to the newly imported file.

  3. Open the newly imported file in the Finder (Choose “Show in Finder” in DT).

  4. Drag and drop the file into Sente (I will have Sente leave these files in place and simply link to a reference in Sente).

  5. Use Sente to create the citation and to create notes for the file.

  6. Drag and drop the citation and complete notes from Sente into the linked DT annotations file.

I could do all this in DT, but Sente may help with the citation creation and I do like the way it handles notes, so I think this may help in the workflow.

Because I have no real experience with this, I’d appreciate any feedback on potential drawbacks or possible enchancements to this workflow! I realize this would not work for many other purposes, but my main purpose is to have all my research documents in one place and be able to easily access a good set of notes for any of these documents.


Thanks happyscholar, that was useful as I’m trying out Sente at the moment. Frankly it’s sleek and ultra-configurable but seems incredibly unintuitive, with inadequate documentation for how to do crucial tasks. Have you refined your suggested workflow? It seems pretty good to me (as I prefer annotations to be in one single rtf note, rather than a series contained within a folder, as achieved by houtthaker’s script ). However, I might go back to using Skim for annotations, as that offers the possibility of exporting a pdf in which highlights are visible to DevonThink, and this isn’t possible (AFAIK) with Sente.

Thanks for your interest in this issue. I’m sure you won’t be surprised that my thinking has evolved since I last posted on this subject. I started to use Sente but then realized there are many things I want to read and annotate much more quickly. I stopped using Sente and am not sure I’ll return to it (one thing about Sente I particularly didn’t like is that it does not keep the annotations in the exact same order as the text, but my main concern was speed).

Despite my concerns about it not being permanent, I’ve been using DT to highlight passages in pdf documents. If I want to comment on them, I create an annotated document and copy and past passages and comment on them there. It is very quick, and I’m finding that speed is important to me.

I am concerned that all/some of my highlighting in pdf documents in DT will one day evaporate. I’d be interested to know if this has indeed happened to people and if there is a way to prevent it.

That would be terrible! Do you have some reason to think that might happen, or do you just have a healthy mistrust of computer software? As far as I can see, DT highlights in a manner similar or identical to Preview; so the highlight information should be written into the pdf file itself, and stay there indefinitely. I’m no expert though - someone else might be able to offer more concrete reassurance.

DT uses standard OS X tools (PDFKit) to make annotations, and these should be viewable/editable in Apple’s standard application - Preview. There’s a high probability they will also be viewable/editable in Acrobat - dependent on what Adobe might change in future releases. Like any software, what works today can be broken with the next release. Thus, my practice for markups, annotations, and notes that really matter is to (a) save those notes someplace outside of the PDF (e.g., use Skim to print them to an RTF), and (b) use some method to have my notes indicate where in the PDF the note refers. For example, I use my own custom scripts that record the page where an annotation links and a searchable link back to that text. Thus, if the annotation ever disappears from the original PDF, I can back track to where the note would have been. Beside being belt-and-suspender data assurance, I end up with RTFs that contain proper references that can be used for later writing in Scrivner, etc.

Yes, I’ve read enough cautions like Korm’s (which I very much appreciate BTW) to make me realize my strategy is not the best. If a quote is particularly important to me, I do copy it to an Annotations file. I’m always open to new ideas!