Best practise pdf- Obsidian + Devonthink

I am currently using Devonthink as my main repository for pdf. I have the Obsidian Vaults indexed in DT. All the highlighted and summary going into Obsidian as notes.

Now with the new functionalities implemented in Obsidian with 0,10.8 ref pdf it seems everything can be done in Obsidian. What do you think? This will increase obsidian’s Vaults dramatically too.

Thanks for your input especially for those using both applications

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Hey there,
I also use both applications (+ Zotero) but I don’t think, that the pdf viewer will change very much for me. It’s lagging (maybe because my mac is 7 years old…), no annotation or searching for text. Obsidian won’t be as powerful as Devonthink and it does not need to be. They have different use cases.

My pdf approach: pdfs are managed by Zotero in a webdav folder. I annotate pdf with notes and sometimes highlighting and extract them with Zotero. Then I paste the extracted notes into the corresponding literature note in Obsidian. That way I’ll have a direct link for each note to the specific page in the pdf. Of course I could use Devonthink to extract the notes, but I want Zotero callback links not Devonthink links. Only for the case that I won’t use macOS anymore.
The references/pdfs and the vault are indexed by Obsidian.

Ty fou your input. I dont use Zotero. I have also indexed the Obsidian’s vaults within DevonThink. I suppose I can do exactly the same using DT, extracting the highlights (summary) from a note and copy the link to Obsidian, that’s being done withhold the need of a reference manager. Am I correct?

Edit: I wrote lengthily because I also wanted that other people know how to do it. Of course you’d already know it.

Actually it is easier if you just move the dt-item and not copy & paste the extracted summery.

For people who wants to know more detailed:

  1. Select the annotated pdf. Then use the summarize function in the menu bar of DT via Tools -> Summarize Highlights -> as Markdown
  2. Select the new md summarization file (in DT) and move it to the indexed Obsidian Vault folder (also in DT)

Now you have the notes as a md file in DT and Obsidian. The good thing is, you have a link for each annoted note to the corresponding pdf page, so you only need to click in it in Obsidian and the specific pdf page is opened for you in DT.
To clarify: not only highlightings but annotation notes will be extracted too.

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Yes thats magic ! Tyvm

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What do you use DT for that you don’t use Obsidian for (and vice versa)? I noticed that:

  • DT’s wikilink suggestions aren’t as good
  • DT’s pdf interaction is excellent
  • DT is a bigger app, and I’m a little daughted by the whole “database” thing. Do you have any recommendations? Can the database be stored in a cloud folder? Or does it have to be on your physical harddrive?
  • If you use both, your Obsidian Vault is located in the “md” file inside the database file?

Thanks! -Erick

I don’t use DT any more.
I used to, and had a very bad experience. Had an older version on my old computer, which eventually broke – so much broke that I could not run an updater on it any more. I tried to delete and reinstall, but the new version didn’t recognize my old database. So I just had to manually mine everything out of the database, which was a nightmare.
Just my 2 cents; if I did use it again, I would make sure to export things regularly. I wasn’t very good about that then.

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Yes, I know what you mean. Devonthink is a very versatile tool and that can be really daunting. The good thing is, that you do not have to use “everything”. Just put some files in some folders which makes sense to you and let the search magic happen.

Can the database be stored in a cloud folder?

Yes, namely iCloud, Dropbox, Cloudme and Webdav. It’s “hidden” in Preferences next to OCR behind the “>>” sign.

If you use both, your Obsidian Vault is located in the “md” file inside the database file?

No, because that’s not possible. For clarification: there are two types of getting files and folders into Devonthink.

  1. Importing: DT put the files and folders in its own database
  2. Indexing: DT indexes the files and folders, but doesn’t put them in its own database.

That’s why we are indexing the Obsidian Vault Folder. For example your obsidian vault is located in /Documents/Vault. To index the vault click in the menu bar of Devonthink

File > Index Files and Folders…
Search your vault folder and “open” it.

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Thanks for sharing your workflow. Really helpful for figuring out what works for me, especially regarding the division of labour between DT and Zotero. I like your futureproofing mindset of not locking yourself to MacOS. But if I understand correctly, for that workflow to work, it is crucial that you let Zotero manage your pdfs and that means you can’t have you pdfs in the linked attachments folder but you need to let Zotero put it into its own folders, right? More specifically, I think this is what is required for the Zotero backlinks to work.

I don’t like this approach because I want to have all my pdfs in a single folder, which makes them easily accessible on any device, regardless of what software is on it. So I’m currently using Devonthink backlinks, basically trading your future-proofing against flexibility in how/where I store my pdfs - in a sense future-proofing in case I stop using Zotero :wink:

Anyway, the next thing I need to figure out is how to best take notes while reading and highlighting the pdf. I know there are a number of good workflows out there, but they all seem to assume a linear work flow: once you’re done reading and highlighting, you do some extracting and converting and voilà, you have your highlights and notes wherever you want to have them (even the excellent script by @ryanjamurphy seems to assume linearity). But that is not how I work. I often go back and forth between multiple pdfs, reading and annotating a bit here and there and then re-reading and annotating somewhere else, so I’m looking for a solution where the annotation file is readily accessible in both DT and Obsidian simultaneously so that I can do my stuff in either DT or obsidian as it suits me.

Why can’t I just work in one of them? I’d love to, but Obsidian lacks pdf annotation and highlighting and DT is not as good for linking your thinking and building a second brain, so any thoughts that are not direct comments on the text in the pdf go into Obsidian, but in the annotation file for that pdf (so that they stays close to the text that triggered them).

So, I’m finally getting to my point/question: I just discovered that devonthink not only supports the usual pdf annotations (that are stored in the pdf) but also a separate annotation file for each pdf (in fact: for any file) located here:

image

So whatever you type into the Annotations field will be stored in a separate file. Markdown is supported (I read somewhere that it is MultiMarkdown v6, hope that is compatible with Obsidian…) But from what I understand, I cannot choose where the annotation file is stored (indeed, I think it resides in the database), so it appears that I can’t put it into the obsidian vault. Is this correct, or is there a solution?

The script you linked to actually summarizes the file’s highlights as the annotation file. So, three things:

  1. Careful, it’s semi-destructive if you already have an annotation note attached. I think the previous annotation note will still exist, but it’ll be disconnected in favor of the new summary. (There’s a prompt to that effect.)
  2. You can specify where the resulting summary goes. I put mine in a folder in my DEVONthink-indexed Obsidian vault.
  3. You can select new annotation notes at least via scripting. It should be pretty clear how to do so from the script you linked!

So whatever you type into the Annotations field will be stored in a separate file. Markdown is supported (I read somewhere that it is MultiMarkdown v6, hope that is compatible with Obsidian…) But from what I understand, I cannot choose where the annotation file is stored (indeed, I think it resides in the database), so it appears that I can’t put it into the obsidian vault. Is this correct, or is there a solution?

I work similarly to you, so what I ended up doing was creating a smart rule in DT that moved all new annotations in the default annotation folder to a folder in my indexed Obsidian Vault; that seems to work pretty effectively and gave me the best of both worlds. You can then type in that annotation window to your heart’s desire and the changes are updated in Obsidian. One thing I have noticed is that DT can sometimes get confused if you make a lot of changes to that file outside of the app, but otherwise I haven’t really run into issues.