I am in the deep research synopsis stage for a book project I’m working on. I have collected research as plain or markdown (MD) text, PDFs, and webpages. Everything is indexed in DevonThink and the book is outlined and will be written in Scrivener.
What I’m experimenting with is using Obsidian or Roam Research to show connections across all of my notes or narrow it to showing connections only within a particular note or folder.
I’d like to think that Obsidian will serve my purpose because it avoids an expensive subscription and is portable and secure in that everything is in plain or MD files.
But, unless I’m missing something, the graph function in Obsidian shows all connections across all notes. This is problematic in that with hundreds/thousands of notes the graph is nearly useless. I’m not able to filter the graph to a particular folder or note. For example, I have folders in Obsidian matching the chapters in the book so that I can draw connections within a given topic (chapter) to create the sub-headings within a given chapter.
From my reading, it seems like Roam has the ability to graph all notes or to graph more narrowly:
Note that there are two graph views in Roam Research. The first is the main Graph Overview that you can see in the left menu. It shows you the connection graphs of all the notes in your database. The second is the graph overview for individual notes that you can access by clicking on the graph icon on the top-right. This only shows the connection to note that is currently open. I love the note-based graph overview as it allows me to dig deeper into connections of a note or idea that I am working on. (https://www.appsntips.com/primer-roam-research-build-roam-graph/)
Those of you who have tried both, am I correct? And if so, should I have major concerns with using Roam Research?
By the way, there is a pretty good video about Roam. There is a bit of a “commercial” at the end but it is a good video. https://youtu.be/vxOffM_tVHI
Obsidian has the ability to view the graph based on a note. They call it “local graph.” You access it from the three dot pull down menu button on the top right of the note. You can then adjust the view based on layer of connections. I think it defaults so you view just the notes connected to the note you are looking at. But you can then view second level connections-the notes that connect to the notes that you’re currently viewing.
Filtering by folder is a popular feature request and I would be surprised if we didn’t see it very soon. The roadmap Trello board shows “graph filtering” as something they are currently working on.
I admit, I’m really excited about this. Not only will this help me make connections across concepts (Medici Effect, which involves innovation that happens when disciplines and ideas intersect) but it will help me put the research into a coherent flow. When you have a lot of research articles this can be a challenge. I think this will help!
My Obsidian vault is also indexed in DevonThink in the same research folder as all of my other research documents, which have some folders by topic. I like making the manual connections because they grow in my thinking as I do so and relying on machine learning is less than optimal. I think the two combined may in fact produce the best overall results.
Additionally, I find that the combination of text connections and the Obsidian graphical representation stimulates further thinking. Text connections alone don’t always foster that kind of thinking. Likewise, only making manual connections via text will miss things that DT may identify that I miss.
I believe the program will find places where you have mentioned a concept but didn’t link it. You can then go through and create a link with one tap. This should help those who are not diligent and lead to emergent linking of concepts. You show backlinks (what they call them) on the right pane. That said, maybe I am misunderstanding what you mean.
EDIT: Obsidian calls them “unlinked mentions” and you can see them under the “linked mentions”
I’m not OP but my workflow is probably very similar to his: open DEVONthink, choose File > Index Files and Folders… ⌥⌘X and index your Obsidian Vault(s). Your Obsidian documents will then be indexed into DT, which means you will benefit from DT’s powerful feature set when working with your Obsidian vault(s) in DT.