DEVONthink + Obsidian

DEVONthink
37

This very similar to what I do – and yours a really sound approach! I think that what ‘note’ means differs for us a little.

DT contains all resources (PDF, images), often drawn into a project group by smart groups. It ALSO contains any project output: sometimes planning files (outlines, Scapple docs, mind maps), partial, full, edited drafts, and published final work, and so on.

Obsidian contains all reading notes (often, my reflections and processed reading/thinking on the resources stored in DT), broken down into concept, people, and reading notes (the latter tend to be longer, and break down an entire book, journal article, etc). Some of these are organised into larger structure notes (e.g. the ‘English Civil War’ might have 10s of notes linked to it, of events, people, related concepts).

Then when I come to write the outputs that are stored in DT (like you, long form in Scrivener), I will refer to my ‘knowledge’ stored in Obsidian about the texts, people, concepts, or reading. I’ll draw the resources from DT.

On a good day, some writing emerges. On a bad day, I fiddle with my apps or spend more time on tech forums than is good for me – when I should be writing… :wink:

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38

I was trying to squeez my mind what those links and organizations in Obsidian can help you for the actual writing. My undersanding is that the links connecting the notes will not make it into the actual paper you are going to write. Do they?

39

@SebMacV and @Dellu I find how you use smart groups very strategic, and it solves my doubt: how do I organise my contents without siloing them?

It makes sense, maybe I can test it in place of Obsidian.

As for backlinks (in Obsidian), I use them for for the followings:

  • to let some cues to my future self (I don’t mind of orphan links: they are fine)

  • to relate one note to another one in order to remember to leave to my future self some context I don’t need right now, but maybe I’ll need in the future

  • to relate one note to another one In order to build a path, a chain of thoughts

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40

I don’t sort by project, but by topic. It is fairly top level: I have 3 main fields of interest (thus 3 groups), then slightly more narrow sub-topics within these groups. Some sub-topics are very big so then I get quite granular. This could go on for quite a while so I’ve implemented a 4 tier rule.

My issue for Obsidian is my vaults are at the top folder level, but I want my Obsidian beaver water notes in the beaver water quality folder. If I did set vaults up at the subfolder level I’d end up with lots of vaults and isn’t practical.

I don’t worry much about my note files mingling, prompting new ideas, and that stuff. I like navigating by folders but I use search a lot and usually scan through what DT has picked up in case there’s anything interesting.

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41

From the list of uses you mentioned, I think the idea of “chain of thoughts” is really fascinating if Obsidian is actually fit to do that. Tags both in DT and Obsidian are also used to chain up ideas across notes.

You know, I am also very curious on how people productively use Obsidian. I am, however, very skeptic of links: at least in a way most people are using them. They are cool stuff: nice to play around. But, I don’t think they are really that relevant, or sufficient to fully express the fully complexity of relations (associations) betweeen two ideas.

Assume you link a note about [[carbohydrates]] with [[energy source]]. What does that mean? Links good for sending of the reader to a tangential topic; or to remove the burden of explaining everything in a single prose. But, I don’t think liking notes sufficiently mimics the thoughts or ideas going in your mind.
If there is a real link between ideas, you have to explain it with prose: not by links. Links do not tell sufficient story.

  • I think the way people are using (as in the zettel community) links to cut down a flow of ideas into separate notes is just a waste of time. We need to think of the purpose of our notes (writing) ultimately. If our purpose is to communicate, to publish, etc, you are better of laying down the connection of ideas in prose, than linking them.

I was reading two blogs on the use of Obsidian: one by Danis Tod: [Denise Todd]( 8 Factors for Effective Use of Obsidian Tags, Links, and Folders | by Denise Todd | Medium, and the other by a person known as Tim ( [44 Identity - TIM - Obsidian Publish]( How I outlined my brain (literally just use all of the organization techniques at once) - TIM - Obsidian Publish). Todd laid down his points in a single extended text where all the relevant points are discussed in one page. Tim on the other hand, never fully elaborates a point; simply puts snippets of text in one note, and hyperlinks you to the rest of ideas.

I find the latter extremely exhausting to follow because the links disrupt reading; and attract my attention. And, the ideas are never fully workout in a single prose. I am forced to click and jump around rather than sit there and digest the points presented there.

For that, I find the excessive use of links to be extremely counterproductive. The problem would further exacerbate for academics because these hyperlinks are not going to make it into the actual publication. A systematic tagging and powerful searches seem to work better.

I would like to hear if I am wrong here.

What your experience with links?
Do you actually find the links useful for actual productive work?

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42

Let me take a stance opposing the impression that some voiced saying that Obsidian does not add a lot on top of DTP. I’m a user of DTP since like over 10 years now, and Obsidian since it was first released. These days, for day-to-day, operational work (tracking of meetings, research for my dissertation, task management) I’ve completely switched over to Obsidian. I use DTP basically only as a data grave for my emails since its search functionality is far beyond what I can do in Obsidian, and way more performant. At any point in time, I’m having like 2M documents in DTP, mostly emails, that I can very quickly search through.

So for content search, I’d use DTP over Obsidian any time. I’m not using DTTG as until now, for over 2 years, it has not been able to successfully synchronize even one year worth of emails. DTTG is a dead fish for me. But DTP is great for what I am using it for…

…which is not a lot beyond search for mail content (for document content I just can rely on Apple’s Spotlight anyway).

Enter Obsidian. Do not mistake it for a markdown editor only. That doesn’t do it justice. The idea behind is “Linking your Thinking” - you essentially create a network of your information, and it allows you to navigate that network. It is an ideal tool to stay on top of things - be it for research or for daily operational work.

One big advantage is its easy extensibility. You can easily add your own code. For example, for my daily meetings, I wrote a simple script that shows me, in a table within the current meeting note, all meetings related to the meeting I’m currently leading, past and future, depending on the invitees etc. I develop this code like once, and then have it used by templates for meeting notes. When I’m having a new meeting, I just add a note to my meetings folder, and because I can specify on a per folder basis which template I want to use, I’ll have everything available to me at that point.

In other words, on top of being a markdown editor that lets you manage your network of notes, it also is a database that you can query within your documents.

As another example, when I’ve my 1:1s with people working for me, I can easily see what were not only the last meeting notes, but also the tasks these people had to work on. Because of the query ability, you can have, in your notes, dynamically all tasks from any other note assigned to anyone you want, and click on them to then see those notes. It is very interactive.

I know I can sort of extend DTP, and I’ve done this quite a bit. But typically that are just scripts that I have to manually call, while in Obsidian, you can have them sitting right in your notes for you.

For my research, I’ve a full workflow that I integrated to have Obsidian notes feed into LaTeX. You can get those scripts here.

Just yesterday, I was able to easily connect Obsidian as a data feed for my blog. You can read about it here.

I think the biggest point for Obsidian is its community. There’s a load of extensions that people build for just about everything - even DTP. And you can easily extend it yourself.

Also, Obsidian is completely up to you when it comes to how you want it to look. Because it is all Javascript, you can change the look and feel completely by stylesheets. Compare that to DTP, where the simple request I had a while ago, to not have things in the Trash being strike-through (because I can’t read those things there just because of this), and I was just told, nope. Not happening. No configurability planned. Really? It’s annoying. Like you cannot even define default views for dynamic groups. Every single freaking one of them you’ve to add your column selection and order yourself. Seriously?

DTP is like old fashion we tell you guys how to work with our software. Obsidian is like, you tell us how you want to use it, and actually, we give you the tools you need to extend it in any way you want. That’s a competitive advantage that is probably the biggest challenge to DTP in the long run.

Obsidian vs. DTP, for me, is Sharing vs. Telling.

Also, think about how DTP forces you into their data model of “Databases.” Yes, you can index files/folders, but ultimately you’ll end up using some “Database”, within which everything has a naming convention that’s just as useful as parsing your Time Machine sparse bundle. In Obsidian, there is nothing of the sort. It’s files and folders, that’s it.

So where do I see DTP? DTP has persisted metadata about the things that it manages. That makes it fast when it comes to a gazillion files. Obsidian, at this moment, does not have that. But. But. That does not mean it can’t do it - it already has a workspace cache, etc. This is just a question of time. There is no limitation really telling it is not technically possible.

Another big advantage of DTP is the number of file types it handles. I’ve never even had the idea to start writing notes in DTP (also, because the Editor is like the worst thing I’ve seen in a long while; again, the UI of DTP is like 1990s). But managing PDFs etc., automating on top of them (e.g., all my OCR runs through DTP’s Abbyy license) is really top notch.

Maybe I’d put it this way: Static content: DTP. Dynamic stuff: Obsidian.

DTP for me is a filing system. A very clever (set of) shoebox(es) for paperwork, with excellent search functionality, plus some automation when it comes to into which box to put stuff. It’s like ELO on steroids.

Obsidian, on the other hand, is a control center, a research tool, an idea management tool, a living organism, a second brain.

DTP is my long term memory.

Obsidian is my short term memory.

Just my 2c,

M

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43

Let me start by saying I hate how obsidian looks (many more aesthetic apps), but compared to devonthink to go obsidian looks much better.

The biggest benefit for obsidian for me is the daily note and calendar feature. There is a calendar view and when clicking the date it brings up that day, or makes a new calendar dated note with my template. Where links and backlinks come to play is for work. For example when I put on my daily note [[project]] task completed with [[person]] this is where I find the power. So when I go to my Project note or my person note I now have a completely interlinked reference for all mentions by project, person etc. This is very powerful as you go to a meeting and can quickly see all notes with mention to a certain project, work group, person, etc.

I don’t find linking for thought that useful however.

And the most important part of obsidian is it actually works on mobile where DTTG is a second class citizen and more of a reference than a work app.

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44

I’ve taken the time to gather my thoughts in a more organized way (hopefully). See here:

http://www.mnott.de/devonthink-pro-vs-obsidian/

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45

Great write up. I agree with nearly all of your points. I do like DTP ability to OCR with ABBY and summarize highlights so I have actually switched from Zotero for this. I don’t think obsidian will be at the level I want, but with all the new pdf search plugins coming (including one with ocr) we may see this in the future.

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46

Interesting discussion.
I am curious for those indexing Obsidian in DT.
Do you have a separate Obsidian Vault for each DT database?
I am generally fine working completely in DT and DTTG. There are a few areas where I get a little chaotic and that’s task/to-do management and scheduling. That’s not really DT’s brief TBH and I haven’t found a way to integrate any other apps to help with that.

My DT databases are divided by specific project for work (as a freelance TV/Film professional every project can be slightly or wildly different) and by subject for personal stuff (finance docs, creative projects, a scrapbook)

Not all of those would need what Obsidian offers but the calendar and task management are intriguing for the work side as well as the personal creative side.
So, do you have a matching vault for each database?
Or am I misunderstanding how that interchange works?

47

I use DT as a library for web archives and PDFs. Obsidian for notes. I also index my Obsidian vaults in DT - which makes it possible to search both the archives (library) and vaults. For me Obsidian is lighter and easier to use on multiple platforms.

I get a lot of benefit from the “local graph” feature in Obsidian, which I set to a focus level of 2. This way I can see concepts in a broader context. I also have a “note completeness” factor using a garden metaphor, using tags such as #seed, #sprout, #plant, #bud. (Previously used labels in DT) Using Groups in Obsidian I color-code these tags so that in the local graph I can see at a glance which notes contain developed ideas and which ones need more work.

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48

Because I use DTG mostly for emails, I have typically one database for like 5 years. I have one single database for documents, but these are not inside DTP, but are indexed off my file system. My OCR process, for example, picks up files that end up in one folder, does the OCR through Abbyy, and then moves them to another.

Honestly, the OS itself, for me, is good enough to find and manage files.

In Obsidian, I have started using multiple vaults, but ended up having a main vault which links in the content of other directories using symlinks. The reason for that is that some of the content that I produce goes to folders I’ve shared with my teams, e.g., using OneDrive, other content sits in its own git repositories.

I’ve one vault at the moment that I share via OneDrive with some collaborators, who have their own Obsidian installation pointing to that vault. That vault I don’t use directly, but have symlinked it into my main vault. One reason for that is that if you share a vault through OneDrive, Dropbox or the like, you’re also sharing the .obsidian folder, which means, if you change your look and feel, you change it for everyone.

It makes sense that you have a database per project in DTP, particularly if you would for each have a different file storage strategy. Again, I don’t use DTP for this kind of stuff, since I am much better off just using my file system. One reason again for that is that my project folders often contain a humongous amount of content that I don’t even want to have inside a “database” - think about, again, code that is shared through git. I’m not going to put that into a database, but it is still part of the project context.

Of course, you can link everything together; I’m just very used to simply using the file system for everything; hence Obsidian works better for me, as it never even attempts to come along with its own storage idea / “database”.

Oh and one more thing: I explicitly don’t buy into this idea of having everything in one directory, that some of the Obsidian folks follow. I’m too old for that probably, I prefer knowing where everything is. My file system is how I orient myself. Plus, I have folders shared with single team members (personnel review, etc.), which go through e.g. OneDrive, and only me and they can see it. One plugin that’s very useful in Obsidian is “Folder Notes.” Essentially, you can put a .md file into your folder (with a dedicated name, e.g. ‘- -.md’), which will then not actually show up in the folder tree, but which will be shown if you just click on a folder. I use that quite a lot, and within those, I’ve then little scripts that aggregate the content beneath them. I’m using that extensively for my dissertation, to re-implement the “continuous view” that Scrivener offers out of the box. I actually first had the idea of auto-generating those “Maps of Contents” (MOCs) using my LaTeX script, and later found “Folder Notes” - and configured Folder Notes to use the same file names as my Map of Contents generator users. That’s why in my screen shots you see quite a number of folders underlined - they all have those special notes sitting inside them.

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49

Thanks @eMaX. That provides lots of context to explore and consider whether Obsidian would be a lift up or a drag.
For many work projects I have to use whatever fileshare has already been established (gdrive, dropbox, onedrive) and I don’t bother with tracking that stuff in DT other than bookmarking important docs, until the end. I have no control over what other people do in those docs or folders.
At the end of a project I do grab final copies of as many docs as I can to import and tag them in DT.
That comes in handy for new projects where I can reuse spreadsheets or calendars as templates or see what NOT to do.
Then I import all the email into the project database and archive it.
I think it’s time to give Obsidian a spin to see if it helps with planning and task management, ideally to the same extent Devon helped with document and note organization which was A LOT.

50

Perhaps I am being dense… is the only point of paying for Obsidian sync the versioning and encryption? Because placing the vault in iCloud syncs it across all devices fine.

51

This is correct. I don’t get it either. I am synching just fine both with colleagues - using Dropbox equivalents - as well as git, which gives versioning anyway.

52

I bought it to support the developers, ensure encryption and commit to a test (that’s a psychological trick I deploy sometimes to make myself test things properly).

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53

I agree that linking to entities (like [[energy source]]) is often less useful. Instead, a note could be marked with a corresponding tag or linked to a structure note where the tag/structure note represents this entity.

IMO, links between notes work best when they are accompanied by a “link context”, i.e. a description of why the link has been actually placed.

If the link context isn’t too complex (requiring a more detailed explanation), the use of link types can be very powerful. Link types are like attributes/tags for a link which describe or categorise the nature of the link relationship. As an example, in case of wiki links, the resulting “typed links” (aka “semantic links”) could look like this:

[[supports::LINK_ID]]
[[refutes::LINK_ID]]
[[based on::LINK_ID]]

These typed links (and any accompanying link context) would often also represent the flow of arguments that you would make in your written article/publication.

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54

I’ve written here, among other things, about my integration between Obsidian and LaTeX. That code is here. I’m using a parser that you can easily extend; hence when it comes to e.g. parsing out some things to not have them in your final publication, that should be no problem with that approach.

I’ve not yet used wiki links within my dissertation, but probably will. In that case, I’ll anyway add a line to my parser to remove those links before passing the content on to LaTeX.

HTH,

M

55

I use and enjoy both programs for their strengths. I find their strengths lie in different areas for my personal needs and workflow.

DT is excellent at sorting, storing, classifying, and finding potential links between different files. But it is not a good writing environment for me. Obsidian excels at customisability, working with markdown, and quick linking. But is not a good ‘everything bucket’ for organising non-markdown files.

I personally find it helpful to have a distinction between where I keep other people’s thoughts, and where I keep my thoughts. So I keep my thoughts in Obsidian and other people’s thoughts in DT. I know when I open Obsidian I’m only going to find things I have written myself. It’s helpful for getting the right mindset for the type of work I intend to do that session.

I also simply vastly prefer Obsidian as a writing environment. It has many more available hotkeys than DEVONthink, which I can assign to suit my personal idiosyncrasies. I find adding links much more intuitive - when I type double square brackets the program suggests autocompletion for the link I’m adding, and there’s no futzing about with the mouse. DT has little/no customisation in this regard.

Last but certainly not least, Obsidian has a reliable, app-wide dark mode, and it’s easy to change the appearance of just about any aspect of the editor with community themes and the Style Settings plugin. This is important for me in a working environment - I rely heavily on colour and font to differentiate between different headers, bullets, indented lists, etc when writing. I don’t mind my file organiser (devonthink) looking like it came from the 90s. I very much mind my writing environment looking like a file manager - it impacts my speed of work, if nothing else.

In short, Obsidian is nothing like Devonthink, and that’s what I need when I’m writing vs researching/managing files. I still use both programs heavily, just for completely different things.

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56

You’re right.