Indexed skim notes (minor breakthrough, I think)

I think I’ve had a little breakthrough, in figuring out how to integrate Bookends, Skim and Devonthink. What I wanted was some way to know what I had/have been reading, and see the notes within Devonthink.

Here’s what I’ve just figured out:

  1. Keep pdfs as attachments in Bookends attachments.
  2. Index that folder in Devonthink.
  3. Create a smart group in Devonthink called e.g. Skim Notes, which searches within the folder which indexes Attachments, where “All of the following are true”: “Name matches skim” and “Kind is not PDF/PS”.

The skim file (highlights, underlinings and whatever notes) is visible in Devonthink, but if opened in Skim will lead back to the Pdf itself.

This means, I think, that I can do as much of my simple notekeeping, commenting and whatnot in skim, even if I arrive at that pdf from Bookends, and have the notes turn up (once I have updated indexed items) in Devonthink.
One of the advantages, then, is that in the list view, it offers a dated list of reading progress.

Perhaps most of you knew this already, but to me it seems like a breakthrough.
Now all I need to do is paste the Bookends reference in as a note at the top of each pdf and I have a reasonably coherent system.
I just thought I’d share this, in case anyone else hadn’t figured out this much for themselves.


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thank for your suggestions. I use the same workflow (Bookends, Skim and Devonthink) but your workaround somehow does not work for me. If I create a smart group as suggested no files will show up.

Do you save the Skim-Notes not in the PDF itself but in another file?

You have to export your Skim notes within Skim and then they are saved as a separate file that Skim knows to open when the respective PDF is opened.

Ok, thank you.

Are the notes in the separate note file being updated if you change the annotations in the pdf file within skim?

And do I have to export the notes for every file separately or can I change something in the application settings so that Skim will save the notes automatically in a separate file?

I would really like for DT to index notes, but for the moment this is very usable. Thanks for the tip!

Hi there,

I do not know if you guys are aware of the scripts on this site: … think.html

I mainly read and annotate on the iPad and sometimes also on the macbook with Skim.

My flow consists of:

  • Devonthink Pro
  • iAnnotate on iPad
  • Devonthink To Go
  • Skim
  • Zotero

This means that I keep the .pdf files in Devonthink, and if I’m on the go sync them to the ipad through DT TG and read/annotate on the iPad. I then sync it back to DT, open it in Skim and run the mentioned script which gives me a group with the .pdf and the annotations as individual .rtf files in DT.

Zotero just keeps the bibliographic information and has a l ink to the file in DT.
I use the Kindle to DT script in the same fashion.

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For me it worked better All of the following are true: All matches .skim, plus the rest you mention