Obsidian and DEVONthink Pro 3

Is there a source for text practice in using DEVONthink (Pro 3) with Obsidian (0.11.13 on macOS 11.2.3)?

I am new to Obsidian, even newer to DT.

I don’t (yet!) want or need to modify Obsidian documents (from) within DEVONthink - just store them in its database (so not indexed) and be able to open any Obsidian Vault from its location in the DT item window, work on it in Obsidian and save it when done - consistent with DT’s own management of files and database integrity.


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Hi Mark,

There has been quite a bit of discussion about DevonThink. Did you search and see those topics already? Search results for 'devonthink' - Obsidian Forum

As for storing, and opening any vault from DevonThink, there is the URL scheme. If you right click on a file or run the Command Palette and run “Copy obsidian url” it will copy a link that you can paste in any software that supports x-url-links, and it will open that file or vault.

From: Obsidian Release v0.9.0

  • Obsidian now supports obsidian:// URIs. For the user manual, check out the help doc Advanced use > Using obsidian URI.
  • Remember to use %20 to encode the space character, and %2F to encode the forward slash /.
  • obsidian://open?vault=myvault will open the vault “myvault”.
  • obsidian://open?vault=myvault&file=mynote will open the file “mynote” inside the vault “myvault”/
  • obsidian://open?path=%2Fabsolute%2Fpath%2Fto%2Fmynote will open the file at the absolute path “/absolute/path/to/mynote” assuming a vault exists for the one of the parent folders.

Chris - thanks for jumping in!

Yes, I did look at almost all of those threads… a little overwhelming :frowning: .

I also looked on the DT forum, and here in Obsidian’s (and DT’s) Help

I’m on macOS 11 (Big Sur). And still confused.

I made a new Plain Text file containing this line:


Selecting it all and clicking Open Link resulted in a ‘Vault Not Found’ error.

What I want to do - and I have to believe that URL scheme is going to be the way to do it - is move my Obsidian Vault(s) into DEVONthink 3 and then open and run it/them in(/with) Obsidian from DEVONthink - in the same way, presumably, as I do when I store a FileMaker Pro, say, file inside DEVONthink.

But because that’s (FMP) one file (and not a folder containing Notes, as is the case with Obsidian), I can see how to do so.

In Obsidian’s case (which I love BTW) there is no single file inside the Vault which I can (double-)click on inside DEVONthink; so I confess to being a little stuck until I understand the principle. Then I’ll be on my way :slight_smile: .

Thanks again…

Have you considered indexing your vault into DEVONthink? That opens up many options. Dig a little deeper and you’ll find yourself using dDEVONthink’s Smart Rules to bulk modify data within your Obsidian vault base on search criteria within dDEVONthink.


Thanks, Dan - Yes, had considered Indexing. But I like the idea of Importing as many docs as I can into DT.

Atm, my Obsidian (with which I really am a novice) Vault is in ~/Documents/Data/.

Will Obsidian still know where it is when I Import it into DT - and so delete the ‘original’ Vault and change the path, of which - presumably (?) - Obsidian keeps track?

There’s no real functional difference to indexing and importing. I can see keeping files that don’t have anything to do with Obsidian imported, that’s what I do, too, but you gain so much by indexing anything that would go in your vault, even attachments.

Thanks, Dan! Yes - I know it’s a popular and accepted way to do things. I used Aperture that way for years :slight_smile:

I can see the advantages of leaving Obsidian files where they are and indexing them. But I also want to be able to move them in the Finder.

Now, I’m making a radical rationalization and spring clean of my entire ~/Documents (and ~/Data for that matter) folder(s).

Will Obsidian still know where each Vault is when I Import it into DT - and so delete the ‘original’ Vault(s) and change their path(s), of which - presumably (?) - Obsidian keeps track?

“Will Obsidian still know where each Vault is when I Import it into DT - and so delete the ‘original’ Vault(s) and change their path(s), of which - presumably (?) - Obsidian keeps track?”


Maybe think about like this; Devonthink is a database that builds an infrastructure that creates its own folders and puts your data in them, Obsidian is more like a superstructure that sits atop the data you place in your vault.

So would I be right in thinking that there is no elegant way to include Vaults in DT - except by indexing them as external folders?

I really do not want to do that:

  • in case I ever do want to move Vault data - even if only from one location inside ~ to another
  • because I am working to consolidate all my docs - including Obsidian ones

Thanks, Dan!

YMMV, but I think you’ll run into problems with that method. If you index your vault(s) any folder structure within the vault remains; you can still move things around within those vaults and so can DEVONthink. It’s a best-of-both-worlds thing that breaks if you try to do it the other way around. DEVONthink, by the way, still builds its database infrastructure, you just don’t see it.

One more thing. You might also find a program like TextSoap or Bbedit edit extremely useful at some point. You’ll want all your .md files in a reasonably easy findable way, like a vault folder structure. It has felt like magic to have regex routines crawl through my files and make bulk updates to phrases of text, insert links, tags, etc. This would be much harder to do if they had to be found in DEVONthink’s database. It is still doable, but harder.

It’s hard to tell, but I think it is formatted incorrectly. It looks like your URL is pointing to a full path file, rather than just a vault.

But I think you’d need &file=MyFile at the end of the URL. Did you hand-format that URL, or use the commands inside Obsidian to generate the link?

Also, it is strange that it is using the entire path /Users/mark/Documents in your vault path. It should be able to just say ?vault=VaultName. (Is your vault called “Data”?)

It looks like if you hand-formatted that link, you may have combined the full-path version with the vault name version. So there is (presumably) no vault named “/Users/mark/Documents/Data/MyFile”


For a real example, this is what I use to open “2019-03-07_Thursday” in the vault “ObsidianNotes”.


But the full path version would be like this, and would depend on my OS, not just the vault name:

obsidian://open?path=/Users/chrislesage/Dropbox/ObsidianNotes/Journal/2019-03-07_Thursday.md (the .md is optional at the end)

Thanks again, Chris!

I finally got this to work: obsidian://open?vault=MyFile.

Yes, of course you’re right: I had miscoded it.

So Obsidian takes care of the rest of the path, does it, because it knowns how to pare anything beginning with obsidian://?

…the commands inside Obsidian to generate the link?…

Not sure where they are. In Settings?

I’m still a little unclear as to how to use that URI to open ann Obsidian vault, please, from within DEVONthink itself? All I’ve been able to manage so far is via the ‘Open Link’ menu item when that string is highlighted inside a TextEdit document. I know there must be a better way.


I very much appreciate your persistence and patience here.

I do believe you’re winning me over :slight_smile: !

I have avoided Indexing files and folders external to DT so far (I’ve only been using it this week… Obsidian for not that much longer) because I just want a kind of tidiness which your experience (much greater than mine) tells me is impossible. I should trust you!

Perhaps I should experiment with Indexing my Obsidian vaults after all. I don’t want to go looking for trouble by trying to do something which Obsidian wasn’t designed to do. It’s just that I’ve moved almost everything currently in ~/Documents out and into DT. My Obsidian Vaults would be exceptions/outliers.

I’m still unclear, though, as to how Obsidian handles its vaults. When I first started to use it, I put Vaults in ~/Documents/Data. I’m surely not stuck with that, am I?

Thanks for referring to BBEdit and TextSoap. I’m a long-time user of both. I have also found PublicSpaces Better Finder… software powerful and extremely quick.

Thanks again!

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There are 4 ways (that I know of)

  1. Right click on a file, or search result file. And click “Copy obsidian url”
  2. Click on the top right button in a panel of a note. “More options” → “Copy obsidian url”
  3. Open the Command Palette by hitting Ctrl-P or Cmd-P. Type “url” and you’ll see “Copy obsidian url”
  4. That command “Copy obsidian url” can be mapped to a hotkey as well in your Hotkeys preferences.

Thanks again. I can see them all!

But I’m still not clear - once I’ve ‘captured’ an Obsidian URI - how to use that URI string actually to open an Obsidian vault from within DEVONthink itself.

So far I’ve been able to click the ‘Open Link’ menu item when that string is highlighted inside a TextEdit document.

I know there must be a better way.

Your help much appreciated :slight_smile: .

Oh I see. I misunderstood your question!

Some apps don’t support or recognize those URLs. For example, in Things or Scrivener, it will format as a hyperlink, and you can just click on it. Those two apps also support their own URLs as well.

Maybe DevonThink doesn’t support the links?


No prob! My fault. And you gave four answers as well :slight_smile: .

Certainly clicking on the string of text (obsidian://open?vault=MyFile etc) in a text file works perfectly.

But whether or not I Import my Vault(s) into DEVONthink, or Index them, as Dan suggests, I want to be able to open them from inside DEVONthink - as (Obsidian) files, rather than having always to open Obsidian itself, which seems to know where the root of a vault is.

Thanking @danlandrum and @rigmarole again, I have now taken your advice, Dan, and Indexed some of my Obsidian Vaults in DEVONthink (now 3.7.1; my Obsidian is version 0.11.13 - on macOS 11.3.1).

It was a bit of a learning experience because I hadn’t understood how closely files and folders which are indexed in DT really are integrated… for instance, I changed one Vault’s name in my DT hierarchy - and Obsidian couldn’t (at first: an easy fix, of course, in Obsidian’s explorer) find it.

I do want to switch from the ever buggier TextEdit (especially with lists, which I use a lot) to Obsidian for all my (linked) notes.

But I remain puzzled - as a perfectionist who really values meticulous organization of all my data (!):

  1. do I embrace and get used to running DT first and launching (files in) Obsidian’s vaults from (within) DT?
  2. if so, what is the best way to ‘launch a vault’… with a URL using x-links?
  3. or do I simply store markdown files in DT for the indexing; and continue to launch Obsidian and access its vaults and files outside DEVONthink?

All wisdom listened to carefully - and with thanks!

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Thanks for the nice words, @MarkSealey. I have Obsidian and DEVONthink open all the time. There are days when I only use those two apps plus a web browser. With that in mind, my vault is always launched. I store all my markdown files in Obsidian and Index them into DEVONthink. You can create completely different taxonomies in each program. I’m not exactly sure what you’re saying in step 3 from your description, but I think that’s closest to what I do; work with files mostly in Obsidian that are also indexed by DEVONthink. I’m generally only in DEVONthink when I need to make mass changes to content in my markdown files, or want to do a particular search that allows me create a new DT group or tag.

There are files that I only store in DEVONthink, but these are generally reference documents, and I pull them into Obsidian notes as x-links.

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