Accessing Obsidian Vaults from DT3

I am playing with Obsidian to get a sense of what its capabilities are.

I would ideally like to be able to import or index Obsidian Vaults into DT3 and use “Open With” as I do with other file types.

Do I Index the Vault folder?

Also macOS does not seem to recognize Obsidian as a valid viewer for Markdown files; I have to choose “All applications” instead of “Recommended Applications” when I use Open With. Can this be fixed to make it easier to open from within DT3?

For those who are using Obsidian, how does it extend what you do with DT3 and how do you link files back and forth between the two?

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Also macOS does not seem to recognize Obsidian as a valid viewer for Markdown files; I have to choose “All applications” instead of “Recommended Applications” when I use Open With. Can this be fixed to make it easier to open from within DT3?

This is not within our scope. You’d have to discuss this with Obsidian’s developer.

Understood - my thought/hope was that some of the users here who use both applications might have some experience or insight. I understand that this is beyond the scope of help DevonTech can provide.

You can’t “Open With” Obsidian at all yet, if that’s what you’re trying to do. I think the devs there will have to enable that before you can do so within DEVONthink.

I index my Obsidian folders in DEVONthink, which enables interoperability between the two.


Thanks - can you clarify that? If you have an Obsidian folder indexed in Devonthink and you want to access it, how do you do that?

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Not from within DT. I open Obsidian and open the file… hahah


Only Obsidian can create links and references between files in an Obsidian vault – mainly because those links are not stored in the plain text files in the vault. Obsidian instantiates the links on the fly.

You can of course access an Obsidian vault plain text file and edit it anywhere else, including in DEVONthink. But you’ll never get the linking features of Obsidian outside of Obsidian.

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But do you think we will get to the point that an Obsidian Vault folder can be stored inside a DT3 database and we can use Devonthink to load the native app and view edit/the files? Just like we can do with DOC, PDF, RTF, and a million other file formats?

As mentioned, that would require Obsidian supporting “Open With > Obsidian” from other apps. I recall discussions of this on Obsidian’s Discord forum, and the developers reluctance for Obsidian being a standalone markdown editor, which supporting “Open With > Obsidian” would open Obsidian up to being.

Put it another way, if you select a markdown file in Finder we don’t get an “Open With > DEVONthink” option do we? DEVONthink is obviously not interested being a standalone editor for files stored outside of DEVONthink.

Anyway, I don’t see the feature on Obsidian’s roadmap either.


I can certainly understand that. But that is why we have x-Devonthink links. If there were an equivalent x-obsidian link capability then that would be ideal.

Isn’t it ironic that an app with a mission to be the ultimate in internal linking does not offer its own links for other apps to use?

Without this capability, what do I do if I have a Devonthink project and among the items I want to include is an Obsidian Vault? If Obsidian only works as its own silo then that seems to notably reduce its usefulness.

I see someone we all know well has already requested this @ryanjamurphy and 31 people have seconded the thought.

For an app that prides itself on making links a first priority, this seems absolutely essential.

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Sorry, I don’t understand what DEVONthink item links have to do with editing or “Open With…” functionality. I’m afraid that’s confusing two things that are not related.

There’s nothing preventing us from indexing the contents of an Obsidian vault in DEVONthink. I do that with my vaults.

Here is the use case

Let’s suppose that I create a DT3 Group about a particular topic of interest. I want to add to that group various types of content and would like to be able to access the content in the group either natively in DT3 or by easily launching some other app from within DT3. So PDF and .md files will be readable within DT3, zotero groups will be usable by clicking the zotero:// link which will open Zotero in a new window, etc.

I would also like to be able to include an Obsidian Vault as a type of content referenced by my group. One way to do that might be using “Open With” to open the content inside Obsidian. Another way might be to click an obsidian:// link to do the same thing and launch Obsidian.

Right now you say you index an Obsidian vault using DT3. But how do you open that Vault while in DT3? I gather you mean you can access individual .md files? Yes but then you lose all the formatting and all the operating links - that seems less than optimal.

Obsidian Vault = a folder. Just index the folder and you’re done.

MD files = plain text. There is no formatting to be lost.

DT also has [[wiki links]]. Just activate it and you’ll be able to browser your files in DT just like you do in Obsidian.

Now, to open a specific files in obsidian: open the app and use the quick switcher. That is the option you have right now.

Interesting - thanks. How about .css or other formatting? Are the Markup features supported the same between DT3 and Obsidian?

Will transclusion work?

Unlinked mentions?

Graph view?

Seems to me viewing in DT3 would lose most of the features which make Obsidian attractive in the first place.

Of course. DEVONthink doesn’t have those Obsidian features because, as mentioned before, they are generated on the fly by Obsidian. We can view the content of numerous applications in DEVONthink but not invoke the display or editing features of those applications within DEVONthink.

A “Vault” is just a folder of plain text documents (with a subfolder for media and one for css). Of course I lose all the “formatting and operating” links when viewing the document in DEVONthink – but I’m not expecting DEVONthink to be Obsidian, nor conversely am I expecting Obsidian to be DEVONthink.

Thank you @korm - that all makes sense as far as what limitations exist viewing Obsidian .md files in DT3. I guess I will remain puzzled why an app which emphasizes that “links are first” is so advanced at internal links but is lacking a major external link capability. So be it.

This is described in the documentation. Did you read it?
The same goes for the MD features supported by DT

I am also puzzled. What app emphasizes “links are first”, and what is that supposed to mean in practical terms?

Again, that DEVONthink cannot display graph and other features of Obsidian is nothing DEVONthink can do, short of buying Obsidian and integrating it into their code.

I was referring to Obsidian’s description of their software in their Help section, noting that “Links are first-class citizens” and overall emphasizing the importance of links in a knowledge base.

I totally understand why Devonthink cannot display Obsidian’s advanced features. I am puzzled why there is not an x-obsidian:// or similar feature by Obsidian to allow other apps to link to Obsidian just like x-devonthink:// allows other apps to link to Devonthink.