Obsidian After All: Book and Research Combined

If I was wiser I would not post this for at least three months. :slight_smile: But, like an impetuous child, I’m going to post this anyway recognizing that I have gone back and forth on this matter multiple times and have posted as much. I could, probably fairly, be judged as being a “compulsive apps switcher,” or accused of far worse. :slight_smile:

But, that be as it may, some struggles and indecision can have value if one finally arrives at a better decision as a result. Aside from the propensity to try out new shiny apps, my dilemma has been compounded by new and rapidly developing applications around PKM, notably Roam, Craft, Obsidian, et al.

So, I’m throwing caution to the wind. I can only ask for the judgement of charity! :slight_smile:

After literally two weeks of work, experimentation and research, including courses by The Sweet Setup, too many YouTube videos, visiting forums, emailing developers, and more … I have moved all of my book related research and the text of the book itself into a single Obsidian vault and have been using Obsidian exclusively for all of my research and writing. Obsidian’s development has reached the point where it is an extremely capable app. which continues to be developed at a rapid pace. One such development is that WYSIWYG is on the short-term of the Obsidian roadmap.

This will eliminate the frustrating clutter intrinsic to writing in markdown, making writing more like writing in Craft or Ulysses.

Prior to this change I was using Scrivener or Ulysses (depending on the type of writing) for long form writing and experimenting with my research notes in DT, Obsidian, and Craft. Every application has its pros and cons.

What I discovered through my experimentation (and frustration) is that by storing both the research and book text in a single Obsidian vault but keeping the research in a separate folder, I am discovering ways to link new ideas and existing research with the text of the book without the need to have multiple applications open for reference and use. This is particularly valuable when using Evergreen notes, which I have starred at the top of the Obsidian file explorer.

Below is a screen shot showing how this is setup. I’m sharing this with the forum because it is strangely cathartic and may be of value to others.

I feel better already … :slight_smile:


I’m curious how this will eliminate the Markdown “clutter”.

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Okay, I think I see what Obsidian is aiming for. Their roadmap says “like Typora”. Typora looks nice as a concept. Still in beta on Mac but seems like it’s been around for a while. I would guess Typora has set themselves a pretty problem. Hard enough to flip the text as you type it with embedded Markdown symbols. But must be tricky to go back and edit.

Like having a Draft and a Research folder, as in Scrivener’s default setup?


Not identical but similar. I was not trying to compare with Scrivener as such. In Obsidian I had a “Book” vault and a “Book Research” vault. But, I discovered that I want to link documents between the two, which cannot be done between two vaults so I decided to combine them so that I can use backlinks seamlessly.

For me I’m looking for something similar to Craft where I type in MD but like Typora ont he Mac, the text is “converted” WYSIWYG, which eliminates the MD clutter.

How do you edit? Does the “MD clutter” reappear when the cursor gets close?

In edit mode, you have standard markdown. In preview mode it goes away. The “problem” with this is that you must:

  1. Just deal with the clutter
  2. Switch back and forth between editor and preview modes, or
  3. Have two panes open: editor and preview.

With WYSIWYG, that problem is eliminated. It is not a show stopper for me. The only real “clutter” that bothers me are web links. If the URL is long you end up with [text](long …………………… URL) in the editor, which I find distracting.

Here is an example:

Why not use a real WYSIWYG format, say RTF?


I can’t do that in Obsidian as everything is in MD. I’m a MD convert and really like having all of my important documents as plain text files. There are a lot of advantages, which have been shared before by others so I’ll not repeat them here. But one I’ve discovered is how fast copying/pasting, backing up files, syncing, etc. is.

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Question - can you explain the separate folder ?? I’m using obsidian similar to you. I’m a teacher and I keep lesson plans and outlines in obsidian (as well as the book notes and PKM stuff) but not sure where to put my files … PowerPoints, keynotes, worksheets etc… they’re currently in Dropbox … but what are you doing? What’s your “separate folder” and what’s in there ??


This. This is exactly where I intend to be heading. Except for PDFs in scientific research.

I’m too easily distracted at the moment to be as focused as you have been over the past months. I thank you enormously for the ongoing insights!


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Prior to making my recent changes I stored my research notes in whatever form (PDF, Webpages, etc.) in Finder folders indexed in DEVONthink). This worked fined except that it was cumbersome to access and to link to my research and writing without multiple applications open and copying/pasting links between them. Workable but not efficient.

I now have those same research assets (and archived published articles) in a research sub-folder of the Book folder. The Book folder serves as an Obsidian vault. This way, all of my research and writing are in one vault so that I can access and link them as needed.

Obsidian Explorer Pane:

As seen in the Finder:

I also use transcluding to “embed” research assets, for example, a diagram or images. The same can be done with another note, a PDF, etc. You can learn more about this here.

As you can see in the screenshots below, there are links beginning with ! which give me direct access to the North Star images that will ultimately be in the published book. When viewing in the editor there is a link to those files in the research sub-folder of the book vault. I can also view them in separate panes or in a single pane in preview mode.

Within Obsidian:

I hope this is helpful.


You are welcome. I’m still in the early stages of learning but I’m getting there. :slight_smile:

@Bmosbacker Wow… this is awesome …. Thanks. I really appreciate the workflow specifics.

I’m still confused with the world vault I think the term is used in multiple ways so I need to explore that … in obsidian I open a vault … but when I sync via obsidian sync that’s also called a vault and it’s a different name … and now you’re calling the folder that you keep the resources in a vault HELP :slight_smile:

You’re in education so maybe I can explain what I’m trying to do and see if you have any insight… As I said I’m a teacher so I have my lesson plans and outlines for each class in a folder in Obsidian, each day is one .md file and I put a link to where the lesson materials are (currently in Dropbox) embedded in the file. Those could be PowerPoints, word docs, pdf, etc… and these could also be sources for me not necessarily for my studnets … but they are all in Dropbox. Are you suggesting these can go in obsidian ?

I love all the hep. Thanks again.

Indeed, different applications and companies use different terminology for essentially the same thing. :slight_smile:

First, when you install Obsidian, an Obsidian folder is created.

Second, after I installed Obsidian I created sub-folders in iCloud under the Obsidian folder and moved all of my material to those folders. Under the 01 Book folder, I created a research folder and other sub-folders of research.

Third, I then opened the 01 Book folder as a Vault within Obsidian. That Vault has the Book chapters AND the research folder.

Essentially, an Obsidian Vault IS a FOLDER on your computer or in the cloud.

The result is that I can access the same files from within Obsidian or any other program.

I also created another sub-folder under research called “01 Assets for book.” For my purposes, “assets” are _media type files, e.g, png, JPEG, media. I store all media type of files in this sub-folder. This naming convention helps me distinguish between “media” and plain text material.

Additionally, I have other folders under research that contain topic specific files. These can be in nearly any file format but whenever possible, I convert PDFs and other documents to plain text and use those in these folders. This makes it much easier to copy/paste and link to this information. For example, I use DEVONthink to convert PDFs to markdown files. It is not necessary to convert the material but that is what I have done.

All of my files are in iCloud. This means that I don’t have to deal with DropBox—everything is in one place for access, viewing, linking, syncing, and backing up.
I hope this is helpful. Please let me know if you have any questions or need additional information.

In short, yes, I have put all of my research material in a folder, which is a sub-folder in my Book Vault in Obsidian—PDFs, Word docs, Keynotes, etc.

PS. @RosemaryOrchard gave this perfect description in another post: “ At the end of the day, Obsidian is a Markdown editor on top of a folder.”

PSS PS: You may find this short article on The Sweet Setup helpful.

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This is the really amazing thing for me with Obsidian. All the files are there for whatever app, no need to export anymore, which just rocks!

I’ve got all my notes, files and research in iCloud folders now, rather than in about five different possible places.

It’s taking me a while to get used to, after many years of my files being locked away in some app or another. Finally, I can be sure where everything is stored. No more wasting time switching apps.

Me too! I’ve finally “seen the light!” :slight_smile:

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The other thing I’m realizing now, after a few months on Obsidian, is that I don’t need 90% of the features in other apps.

Being able to add features as I need them is much better than having a gazillion features that I don’t need.

I’m finding the same thing. There are some exceptions, e.g., tables which are harder in md but I’m finding simplifying is helpful and saves a lot of time. I spent many hours recently converting an entire graduate course–syllabus, standards assignments, you name it … into md files. :slight_smile:

One thing that helped me was that I indexed the graduate course folders into DT and then did a mass conversation where possible to md. That saved a lot of effort!

A Word of Caution: I copied and pasted those original files into a separate folder for this work to protect the original just in case … this is always good practice when doing wholesale changes. I had also made two backups. :slight_smile: