Obsidian and DEVONThink companions

I am a tech writer by trade, and a Medievalist in terms of academic training and scholarly pursuits. I take a lot of notes, and annotate a lot of .pdf files.

  • I am moving 30+ years of notes currently .html and .rtf from VooDoo Pad to Obsidian. These began as HyperCard stacks for my PhD qualifying exams, and teaching notes, and dissertation and journal research, and have been cross-linked from the start.

  • I use mostly PDF Expert and an Apple Pencil on an iPad to annotate .pdfs. They are organized in broad categories via folders, with files names being surname_date_key_title_words.pdf.

  • I do not use a reference manager, like Endnote or Mandeley or Bookends because they are a PITA in terms of exporting the data directly. Instead I log references in a spreadsheet with a citation, summaries, comments, a link to the file in iCloud, etc.

  • I am planning to buy DEVONThink Pro this weekend, and will use it to index the .PDF files. I think I will probably just index them, and not store the actual files in the database.

  • ETA: At some point I plan to go back to school for an MLS /Library School MA. So I want to pave the way now, rather than learn DEVONThink then.

My adoption of DEVONThink is largely spurred by the MPU episode 636 Workflows with Ryan JA Murphy.

Does my plan to pair Obsidian and DEVONThink this way make sense?

Any suggestions about how to proceed?

I am looking at previous similar threads in MPU like this one and this one, too.



One potential issue if you plan to use DEVONthink To Go and PDF Expert on the iPad is that PDF Expert does not work well with DTTG.

There is an ongoing issue for well over a year where changes made on documents in DT’s database using PDF Expert do not save properly back to DT i.e. they are lost after editing. The issue is on the PDF Expert side and has been reported to Readdle multiple times both by the users (I have sent them logs and screen recordings) and by the DT team (who have given them licences for DTTG to test with) but has not been fixed yet. This seems to have been a low priority bug for Readdle to fix and now, of course, they have more pressing matters on their hands.

The issue seems to be related to how and where PDF Expert saves back the file when it’s edited and why it is not picked up properly by DTTG — the DEVONthink team says the issue is with the PDF Expert. Long story short, there’s something amiss with how the file exchange between apps is implemented in PDF Expert.

You can read more about it here.

There are workarounds (sharing from PDF Expert back to DTTG but then you end up with duplicate documents, or using Foxit or Highlights to annotate which work well) but generally DT’s annotation features on the iPad are great so it’s probably best sticking with DTTG’s built-in PDF annotation capabilities as the issue is not limited to PDF Expert.

Things are working well on the Mac of course.


@Medievalist said the plan was to buy “DEVONthink Pro”, which runs on macOS so your concerns are misleading. :wink:

I know, but the post also said:

I use mostly PDF Expert and an Apple Pencil on an iPad to annotate .pdfs.

which led me to believe that @Medievalist might be interested at some point in using DTTG as well as that would make sense to have DT available on both platforms.


Sounds like a plan. My recommendation is you take a look at the excellent ebook “Take Control of DEVONthink” available compliments of DEVONtechnologies on their web site. Also there has been lots of discussion of interfacing Obsidian (and so many other tools) with DEVONthink on their Forum. Good to use that forum as your learning resource.

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What is your experience with PDF Export on iPad without involving DEVONthink ToGO and without importing the files?

@Medievalist mentioned not putting these PDFs into DEVONthink (indexing not importing), so if on the iOS device and accessable can presumably the PDFs can be accessed directly?

PDF Expert works great on its own (and it’s probably best in class) if the plan is to work on documents stored in iCloud (and in fact in any cloud as it has built-in support for Google Drive, OneDrive, Dropbox, etc., even SMB, WebDAV and FTP).


The Take Control book is excellent, and has been of enormous help.

Videos are not as helpful to me as text because I do not see well.

Sorry about your sight. While I still have my sight, I also don’t like videos. Takes too long!

The “DEVONthink” handbook should also be skimmed … read the interesting bits and get familiar with what is there for future use. I have imported a copy into DEVONthink and tagged it as “favorite” for quick reference.

Enjoy DEVONthink.

Make sure Obsidian works well for you before you dive all the way in. I know it works for some hard-of-sight users but others wish it did more, accessibility-wise.

The DEVONlink Obsidian plugin helps bridge notes indexed in DEVONthink.

I recently published the “streaming notes” workflow I mentioned in the show. Apparently it even works for other people!


You might also index your Obsidian vault in DEVONthink. That might provide an advantage when using search in DEVONthink or the “See Also & Classify” feature in DEVONthink to find related entries in the PDFs and your notes. I index a few vaults in DEVONthink – though I only do the editing in Obsidian, out of an abundance of caution probably.

Your reference spreadsheets can also be indexed in DEVONthink.

Good luck with your project,


I index my iCloud Obsidian vault in Devonthink which works really well. I’ve been really enjoying @ryanjamurphy new scripts that he shares above too. A bit fiddly to set up (and requires me to keep my DEVONthink machine open) but it is very cool to markup a pdf on my iPad in any program and have my annotations waiting for me in Obsidian.

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Thanks. I read and listened to a lot about Obsidian last year, and started using it, slowly, in January.

It’s not HyperCard, but it’lll do ;).