Please help with advice on Devonthink workflow


I’m a Devonthink newbie. I’m also a post-grad law student at the beginning of work on a thesis. I have a current workflow using Apple Notes and Hook - but I want to migrate to Devonthink for all of the reasons you’re here too. I need to understand how Devonthink can improve my current workflow and whether my existing routine is no longer appropriate.

Current Workflow:

  1. I’ve been saving my resources as .pdfs in Finder folders by country/subject (legislation, government publications, articles, scholarly reviews, etc.) on my macbook’s hard drive.

  2. I then open a .pdf in Adobe and use the comment functions to annotate my notes and comments - and then save those changes.

  3. I then use Hookmark to hook that locally saved .pdf to a new Apple Note where the entire project is organized.

I use this routine because it is imperative that as I revisit the locally-saved .pdfs and continue to add notes, hooks, references, etc., that the document available via Hookmark in the Apple Note is always pointed to the most recent version of the locally-saved .pdf.

After exporting Apple Notes to DT3 (I believe there is now a convenient tool to do that) I expect that each Apple Note will magically appear in DT3 in the similarly organized nested DT3 folder - and each file will contain/retain the Hookmark links to its locally-saved hard drive copy.

What I now ask myself is whether my Apple Notes workflow still makes sense - or whether DT3 allows me to reduce the workflow, or whether I’m missing something altogether in what I should expect to see after export. I’m worried that I’m going to pull the trigger and either shoot myself in the foot or make myself miserable with more work than anticipated.

Countless DT3 users have been through this sort of research and academic writing scenario - and I’m hoping that one of them can help out a newbie.

Thanks so much and I look forward to any responses.

I store my resources in Devonthink along with my notes
Minimal groups (folders); I prefer tags for organization

I then use Hookmark to hook that locally saved .pdf to a new Apple Note

I’m not a Hookmark user
Devonthink links work for me

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Welcome @markmusselman

Considering Apple Notes isn’t going to update the content in DEVONthink and vice versa, I don’t see the utility in continuing to use it for this process.

You can easily take notes in a variety of formats in DEVONthink - most popularly rich text and Markdown.
You can also explore taking notes about particular documents via annotation files in the Tools > Annotations & Reminders inspector.

This and more is documented in the built-in Help and manual.

Does DT3 eliminate the need for Hookmark as per kind response above? It’s a remarkable app that I thought would provide bi-directional linking solution - but maybe not necessary.

Does indexing in DT3 do the job of always providing access to current (latest) version of file instead? Or the DT3 links referenced?

I’ll get into the help resource tomorrow. Thanks.

You can already use DEVONthink’s item links with documents in your databases. This includes indexed items.

Does indexing in DT3 do the job of always providing access to current (latest) version of file instead?

Indexing is dealing with the file in the Finder so changes saved in the file are shown in DEVONthink.

All sorts of workflows are possible, and in the end we each have to invent our own, mainly by experiment and finding out what works for us.

Having said that choices are very individual, I would get rid of Apple Notes asap. There are much better tools out there. My own method, at present, is to use DEVONthink as a repository for research material, and I keep my notes in Obsidian. It is possible to link material in the two programs. See:

Ryan Murphy writes some useful stuff about knowledge work.

You could also have a look at Kourosh Dini:

For long-form writing it would be worth trying Scrivener, if you don’t already use it:

This also supports linking to DEVONthink items.

But the list of resources out there is endless: Macsparky’s field guide on DEVONthink, YouTube videos by Bryan Jenks on using Obsidian, and those by Nicole van der Hoeven on the same. There is the Take Control book on DEVONthink.

To sum up, there is nothing like the proven scientific method of trial and error for discovering what works. Just play with it :wink:




And just as a follow-up to what I wrote earlier, David Sparks (MacSparky), was a lawyer for much of his life (he has only recently stopped practising) so he knows a lot about combining software and working on legal matters. He is a heavy user of Obsidian, and explains his use of the program in a video hosted by Nick Milo:

You might find it illuminating.

Best of luck with it.

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Thanks Jim - yes, my intention is to leave Apple Notes in favour of DEVONthink. No need to continue using except for quick notes about what my wife asks me to buy at the grocery store!

I’ve read a great deal about using Hookmark with DT, but now that I’ve read about DT’s indexing (and the bi-directional syncing of revisions it provides) I’m no longer sure what additional value Hookmark provides. I love the Hookmark product and have purchased it, so I’ll find some use for it, but just not sure if its bi-directional syncing solve is needed anymore if using DT.

Please let me know if I’m missing something.

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Thanks very much. I’ve watched and enjoyed his unashamed confession of being a lifelong geek. I’m all for efficient processes but my brain would drown very quickly if I tried to engage with his note and file systems and his very disciplined daily/weekly routines. Again thanks for the input - cheers.

Something I believe you can do with Hookmark is link several items together, so that when you select one and invoke the Hookmark window, you can see all the items that are linked to it. This may or may not be useful to you. But one scenario might be that you want to link multiple items to an email, so that when you open the email, you can see all the items that pertain to it.

You’re very welcome.
Bookmark is certainly a good application and if you find use in it, we won’t try to dissuade you from using it. :slight_smile:

yes - multiple connected links is one continued use case that DT doesn’t seem to offer. thanks.

My email is archived in Devonthink
Again, I use Devonthink internal links

Check out the Tools > Document > Links inspector.

Let me add some info on how I use DT3, since it is the result of much trial-and-error, it might help you not make the detours I have or give you some ideas.

The great thing about DT3 is that you can use as much or as little of the functionality as you want. Here is a short summary of how I use DT3 for capturing information that use in my own writing.

Basically, I use it as a universal repository and full text search engine for all things I collect, but not for things I write myself.

Some examples:

Web pages: The best way to capture web pages (after much experimentation) for me is to PDF them as Reader Views in Safari.I created a keyboard shortcut for “Save PDF to DEVONthink 3” as ⌘-P, so for me the work flow for capturing a web page is:
⇧⌘R - Open current page in reader view
⌘P - Open print dialog
⌘P - Save as PDF to DEVONthink3

Downloaded PDFs and other file types: I move them to Universal Inbox that I have in my favourites in the Finder sidebar.

My own writing: After having tried many different writing tools (Scrivener, Ulysses, bear, iA Writers, Apple Notes and others), I have settled on Obsidian as my tool of choice for almost everything I write myself. I use DT Item Links extensively to link to my sources.

I am not as disciplined as others such as MacSparky when using Obsidian, but I find it much easier to use (especially linking between notes) with just the keyboard than most other editors.

For annotating or marking up PDFs I mainly use the built in PDF viewer in DTTG. Works for what I need it for.

Apart from the database I use for that, I also have one where I keep everything pertaining to my personal life, where every letter I receive gets scanned and OCR’d, all my financial documents, contracts, etc reside. The AI helps immensely here.

I also have a database for my email archive, at the beginning of a year I move all my emails from the year before last to DT3 (example: in Jan 2023 I moved all my emails from 2021 in DT3), that way I have a minimum of 1year and a maximum of 2 years in my email account and everything previously is in DT3. I have an email archive reaching back to 2006, fully searchable. Seldom needed, but on occasion quite handy.

I can honestly say that DT3 is the most cost-effective software I have ever paid for (and probably the cheapest on a cost-per-year view) and the only reason I am still using a Mac as my daily driver. If I could get something similar on Linux I would move to Linux in a heartbeat.

Hope this helps.


Some have said this already…

I use Obsidian to do my writing in markdown. I index the vault in DevonThink.

DevonThink is where I put all of my files. You can write markdown in DevonThink if you wish. Some on here do. The beauty is you can try one, the other or both as Markdown is universal.

I use Hookmark particularly for its speed and it creates markdown friendly links in Obsidian.

Apple notes probably does not bring much to the equation, but I friends that really like them.

Experiment and use what works for you. There is no right or wrong way.

This is very helpful. Thanks. You mention that you use Obsidian to write. I’m writing an academic thesis and had assumed that Scrivener would be right for that application because it seems to offer native outlining and navigation options that seem intuitive. Obsidian-at least in the use examples I’ve seen demonstrated- seems less intuitively helpful. Maybe I’ll take another look. Thanks again.

A lot of people use Scrivener for composing their academic work. And Scrivener provides good connections to LaTex. And connections to reference apps can be made. Discussed numerous times on the Scrivener Forum and in the “Scrivener Manual”.

I looked briefly at Obsidian and concluded that while the “cool” kids used it, it is no Scrivener.

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Amen and very true! :smiley: