ISO: Note-taking App that can form a Quick Access Knowledge Base

I am a historian, teacher, and a writer. I am looking for the best note-taking app for my use-case — Or in this case a second brain.

Key Interests:

  • markdown (preference for multi-markdown)
  • note linking capabilities (active within app preferably)
  • tags/smart folders/filters

My issue is this. Whether I am writing, researching or teaching I want quick access to evidence/data. I want to be able to catalogue data in a way that allows quick retrieval but also to be able to link notes together directly so that I can click the link directly in the note. In essence I am looking to create a plain text database with powerful search functions and note linking. One huge use-case for me is that I don’t lecture in my classroom and I need a quick method of accessing data on the fly so that I can answer student questions in real-time. This works relatively well in the app I already use, Bear. But I am not particularly fond of the “folder” (tag) management. I love tags, but not sure as a primary mode of organization. I am flirting with Ulysses (since I have a setapp subscription).

Any ideas, apps, workflows, suggestions?


Have a look at The Archive at

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Wow. How did I miss that one? Was hoping for IOS too though since that is my teaching device. I will check it out though. Thanks.

I use Ulysses for this. 1.2 million words and counting. Folder and tag combo is much better than tags alone.

If you don’t mind me asking, how do you differentiate between tags and folders? Where’s your line? Folders = general cat, tags = clear topics? Just looking for unique workflows.

Folders for projects, tags replicating my keywords from bibliography database.

For reading notes I add keywords in BibDesk and use a script to copy them to the linked Ulysses sheet with reading notes.

For fieldnotes and general analytic notes I tag in Ulysses.

For archival material I add keywords in a Filemaker database and create a linked sheet in Ulysses, also via script.

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You might find this video,Sönke Ahrens - How to take smart notes or his book interesting. It is based on the work of Niklas Luhmann which The Archive software is also based on.


The book is quite good, but …

I use these scripts to link in Ulysses as I prefer something more meaningful than a 16 digit date-time stamp.

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iA Writer! Mac and iOS , 100% markdown with great search, tagging and referencing of other documents within. (Even on export :grin:). See Federico Viticci’s iPad opus for great examples.

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How about DevonThink ? It has excellent organizational (folders, tags, and search) capabilities. You can write in markdown and create document links (within and out side the program). I use the Archive for things that I am pondering and leave my primary references and notes in DevonThink - but it is quite easy to link the two.

I second the recommendation by @NiranS of DEVONthink Pro. It is a very flexible database app for macOS and iOS that can sync data (though I only use the macOS app). DEVONthink can either “import” files (that is, manage files in an internal folder structure in its own database package) or “index” files (that is, work with files that are stored outside the database package but indexed by the database).

I choose to “index” files in DEVONthink Pro so that I still have full control over the indexed files in the macOS filesystem, and I can also browse the files in other apps such as the Finder, Terminal, or Leap, creating what Douglas Barone in 2009 called the “file system infobase manager”: “rather than putting data into an [‘everything bucket’] application and using the ho-hum functions of that app to work with my ideas, I keep my data separate and have best-in-class applications, using higher levels of functionality, work on it. […] By using ‘everything bucket’ applications you give up functionality for compactness and eventually that equation works against your creative process. By working in the file system you use the best app for each specific purpose.”

Of course, what counts as “extraneous” depends on your requirements! In this case, the OP already uses Bear and was looking for different features! :wink:

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