Notes - "Linking your thinking" or "Folders, Notes, and Files" Apps

Wondering if the new-era linked tools for thought PKM style note takers

  • Obsidian
  • Roam
  • Logseq
    are preferred over the older Folder structure style PKM notes apps
  • Evernote
    Apple Notes

What’s your preference now these new tools have been out for a few years?

I now have my Files in Devonthink (bills, tax, reference docs, kids school etc), so this is purely note taking, and for that I find everything adds more friction than eases the world load. Interested in how you’re using the apps and if the modern style has been better than the old school?

I just use both. E.g., stuff in my teaching folders often link to things in my research folders.

My advice: try not to worry about this at all unless you have a problem finding things. :slightly_smiling_face:


After giving it a good go, I’ve decided that “linking my thinking” is more trouble than it is worth. Everyone’s mileage will vary, of course.

I have limited my linking to creating a quick reference table of contents. I can do that effectively and efficiently using Apple Notes, as shown below. Again, this is a matter of personal preference and workflow needs. Creating and managing links across my notes takes more time than anything I have gained from doing so. This is one reason why I use DEVONthink for all of my research. The search capabilities are so strong that I can quickly find any related material without creating links that may or may not be maintained should I export my material elsewhere.


I found similar, and just never seemed to go back to see all the links to “Joe Co-Worker” or a specific action on a project.

I see there’s massive amounts of hype around it, so feel like I’m missing something and don’t want to dismiss the technology. Currently I’m trying Roam Research which seems like a good new-era option, but I feel I’m taking twice as long entering the data to ensure it’s all linked rather than ever going back to those links.

I’ll add that with the increased availability and capability of AI, manually linking documents will become less needed. I can simply have AI scan documents and provide links or summaries as needed. We are not there yet but are getting there quickly.

I use Obsidian exclusively now and yet I use it with over 100 folders. It’s not an either or situation. I also do a lot of linking. I link a lot of my thoughts into MOC/TOC type notes or when they are subordinate pieces of a main note but I also organize notes in folders in ways that make sense to me.

In spite of the scoffing at the graph view in Obsidian I find it useful to find orphaned notes that often can be combined with some other note or are no longer relevant so I use un-linked stuff as a way to prune my note collection.

I also have both a open random note and open a random note from a search button and when I am spinning my wheels at the computer on something and need a short break I “roll the dice” a few times. When I read the resulting note I can often clean it up, add properties in the front matter as I’ve changed by note templates quite a bit since Ii started or improve the note by making a summary at the top or whatever seem appropriate. I can also decide the note was worthless and delete it, About 10% of the time that a note I randomly see can either be combined into another note or deleted. I like the random nature of cleaning up my notes over time and it also gives me an overall view of what I am keeping there I can’t get any other way.

I frequently use my Farley file notes on people and so I do make a point to link their names into everything that is appropriate. I also use some review type task and dataview queries to get a feel for what I’ve been working on and my daily note/journal is also critical for me in finding stuff. I link project notes in it on the days I worked on specific projects and then when I review the project I have a quick overview of the days I worked on it by looking at the backlinks.

I’ve found Obsidian’s smart linking is very good. I can start a link and type a few things and I get a list of choices for what note to link. Most of the time the one I want is in the top 5 options. YMMV


I only have a note pinned with links to a few essential notes related to books, movies, home and work.

I used to add links in every note and blog articles but now I just paste the name of the notes. In case I need to access, I just copy the name and search.

So that’s why reliable search matters. I said I was using Apple Notes, but it is not so capable of searching what I want. Even though I have workarounds the search is not guaranteed.

Now I am moving notes to Bear.

(Usually most note taking apps have basic search functions. I don’t know why Apple Notes really sucks.)

Interesting. I’ve not found that to be the case. I am able to find anything I’m searching for in AN, including text embedded in PDFs, images, etc. It is true, “YMMV.” :slightly_smiling_face:

Agreed of course that everyone’s situation varies.

I agree that the typical huge web of links proposed in many articles takes more effort to create than to use.

I have found personally that there are two specific times when creating links is well worth the effort:

(1) If I plan to discuss documents in real-time, i.e. presenting my thoughts to a client or testifying in a deposition over Zoom- in those situations it is worth the advance organization to create links rather than to run searches which will take more time to find the information.

If you can anticipate potential questions from your client or an opposing attorney, links which let you find specific documents/paragraphs quickly create an extremely powerful impression of information mastery.

(2) Bookmarking large documents - This is somewhat of a variation on your concept of creating a quick reference table of contents. Maybe in some cases the are the same thing. In my work process, a table of contents would link to major sections of a document. Often what I need instead are links to random key paragraphs or key pages to illustrate major points in a case. Thus for example if I am reviewing a 10,000 page document and plan to write a 10-page opinion paper based on its content, then prior to writing that paper it is helpful to create 50 or 100 links to the most critical parts of the source document.


If I have to deal with a 10,000 page document I may just have AI summarize it! :joy: I’m kidding, mostly. :slightly_smiling_face:

I totally understand the sentiment. Even though I need to confirm all of the essential facts, a summary can be a great first-pass or a good double-check that I did not miss anything. In many cases what I need is not really a summary but rather finding specific items within the document, such as “List all MRIs” or “List all diagnostic tests” or “List all surgery operative notes.”

I have been looking for a while for AI apps that can handle such a query and give links to the relevant page(s) within the document. So far this is the best one I have found (It requires a ChatGPT Plus subscription):


If a Notes/PKM app isn’t able to create an automatic Daily Note and doesn’t support backlinking, then I won’t use it. I’ve felt like this since I used Roam, but with Roam, I couldn’t justify the $15 a month cost.

Both features are so useful, that not having them makes me feel hampered.


For the record, I don’t want my doctor relying exclusively on AI to summarize medical research, I’m glad you personally review the research! :slightly_smiling_face:

That looks like a great feature. I have a ChatGPT Plus subscription so I’m good to go. For those who may be interested, ChatGPT provided the summary of this feature, see below.

I have been using the new AI feature in PDF Expert but PDF Ai PDF looks more capable. I’m going to give it a try. Thanks for passing this along!

AI PDF GPT is designed with a specialized focus on handling PDF documents efficiently and effectively. It offers several key advantages over the traditional file handling in ChatGPT, particularly for users who work frequently with PDFs. Here are some of the notable differences and benefits:

  1. Unlimited Document Uploads: Users can upload an unlimited number of documents to their account, providing much greater flexibility compared to the native ChatGPT solution, which limits the number of files you can upload and keep track of during a conversation.

  2. Permanent File Storage: Files uploaded to a user’s account can be kept indefinitely, offering a permanent solution for document storage. This contrasts with ChatGPT’s native file handling, where users must reupload documents for each new session.

  3. Large File Support: allows users to upload much larger files, up to 2 GB each. This capability far exceeds the size limitations typically found in email attachments and many cloud storage services, making it ideal for handling comprehensive or high-quality PDF documents.

  4. Pro Account Benefits: For users who upgrade to AI Drive Pro, additional features are unlocked, such as automatic Optical Character Recognition (OCR) of files and data extraction (authors, titles, file description). These features enhance the usability of the PDFs by making them searchable and more easily organized.

  5. Integrated Chrome Extension: A Chrome extension is available to manage files in the AI Drive panel right next to the ChatGPT panel. This integration provides a seamless experience for users, allowing them to access and reference their PDFs without leaving the chat interface.

  6. Fast PDF Viewer: An integrated super-fast PDF viewer within the user experience allows users to quickly view the reference links provided by AI PDF GPT. This feature ensures that users can easily verify and consult the documents being discussed without needing to open them in a separate application.

  7. Specialized PDF Handling: AI PDF GPT is tailored specifically for PDF documents, providing functionalities such as summarization, semantic searches within documents, and precise reference linking. This focus ensures that users can get the most out of their PDFs, with capabilities beyond what’s typically offered in general-purpose chatbots.

By concentrating on these areas, AI PDF GPT offers a more robust, user-friendly, and efficient solution for managing and utilizing PDF documents, especially for users who need to store, access, and analyze large volumes of PDF files.

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I think it is a good question! I personally found that I spend a lot of effort for the input but have limited output from it. Note taking is certainly valuable and connecting it to known material can also be helpful. But I find myself rarely looking and carefully crafted connected notes on a certain topic I was interested in for a while.

I hope it is different for others.

I’m an “everything bucket” user. I started with files and folders, used Evernote and/or EagleFiler for several years, and now keep everything in Google Drive.

I tag some files, and occasionally link emails with tasks, and documents with events, etc. but I mainly dump everything into one of ten folders and use search to find what I need.

Search isn’t fancy but it has been working for me for 20+ years.

I tried PDF Expert because the idea of not having to upload files to the cloud is appealing. But after using it I suspect their use of the term “AI” is either misleading or hides the fact that it uses a very primitive LLM in order to do the AI query on the local computer. Its responses are very simplistic; it seems more like adding Spotlight search to a PDF document than adding AI chat.

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I use DEVONthink for “Linking your thinking”. So I have not found the need to explore Obsidian or Logseq.

I’m currently experimenting with OBTF (One big text file) with Bike Outliner and a zettelkasten using The Archive, considering of course that BASB isn’t the same as a zettelkasten. Which is kind of strange because Bike and The Archive will create .txt files in one folder by default.

I also carry with me a Hobonichi Planner. Used to have my BuJo but since I bought this planner on December I started to use it instead of buying another blank notebook.

Right now, I’ve settled on Agenda as my notes app and EagleFiler for my everything bucket (mostly for older stuff/archive).

Notes linking on Agenda is only from Client Notes back to the Daily Notes. That is, when I have a long or complicated job, I cut the appropriate paragraphs from the Daily Notes where I did the work for that client and land them in one Client Note, sorted reverse chronologically, first of each paragraph dated back to where I cut it. The backlink lands where I cut the paragraph in the Daily Note for reference.

I made a Template for my Daily Note creation, with the proper ISO 8601 format. Easy to activate and all that is left is to Assign Date on creation; takes two seconds at most for the whole process.

EagleFiler is used for archiving old emails and old files I rarely touch. I’m using Spark Desktop for my daily email client, because it handles attachments correctly as icons in a holding pen. The only time I fire up Apple Mail is if I have to use EagleFiler to archive emails, and to update so iDrive can backup my emails. EagleFiler is Intel only. If version 2 ever is published, Michael Tsai says it will be Apple Silicon Capable.

DevonThink is nice, but benefits most if you have one focused area of study so the AI features can work. My interests are so varied, the AI never could get a handle on me.

I have so many small jobs, and I never can plan for them, I carry a Traveler’s Company vertical weekly planner for basic scheduling.

EagleFiler 1.9.3 - EagleFiler - C-Command Software Forum

The indexer, which is one of the most processor intensive parts, is already native on Apple Silicon Macs, and my experience is that the rest of the app runs well in Rosetta. The full app will be native in EagleFiler 2.0.

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