Adding diagrams to Zettelkastens digression from ISO: Note-taking App that can form a Quick Access Knowledge Base

Continuing the discussion from ISO: Note-taking App that can form a Quick Access Knowledge Base:

For all the Zettelkasten folks out there, especially the ones that just use text files for everything, what do you do about notes that benefit from diagrams, flowcharts, and other image-based pieces of information?

I imagine, the actual index-card based systems can use cut-and-paste. But that seems like time-consuming work.


Agreed. I don’t use a Zettelkasten system; if I needed to do something with reference links I’d most likely use wiki software.

… although the Zettelkasten folks might disagree:

Zettelkasten seems a bit too geeky and requires tending to, which I really don’t like in software. (I don’t use tags either, for similar reasons.)

If you’re interested in delving more deeply you might be interested in the following:

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If you need diagrams in your notes, then use diagrams of course!

The point is to build a library of notes that works for you. Sites like are interesting but no one “owns” the concept or sets standards.

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I think I may not have asked my question articulately. My question was not about permission to use diagrams. My question was how do people incorporate graphical items with their tools. Most of them seem to be based on a library of plain text files.

That was my thought, too. I’m an outliner but there are things about this system that are intriguing to me. Thanks for the resources. I will check them out.

The “tending to” is a good thing. For instance, I take notes in margins and on Cornell-lined paper, then type those notes into my zettelkasten, put in links to valid references, and link other notes to the new note.
Using this method I have many opportunities to think about and integrate the information. Linking to and from other notes relates the new information to things I already know (scaffolding). Tagging can also be a mental exercise, asking yourself where does this apply? What is the focus? How will I search for this in the future? If using something like Tinderbox, TheBrain, LiquidText, Curio, one also builds and remembers spatial relationships in the material. This ties in nicely with The Method of Loci, also known as memory palaces.

The alternative is to efficiently highlight the pdf.

My (as well as others) thesis is that the perceived efficiency of highlighting is not efficient at all if your goal is mastery and retention of the information.

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Just link to a diagram. To view the diagram along with the note, use a markdown viewer like the excellent Marked 2.


Great post, John. I will write more but wanted to note this point in particular. I have long discovered that annotating a PDF, book, or what have you is an important step. But I have to get the notes out of the PDF and put elsewhere (in my case it’s a master outline). It is terribly inefficient to re-read a stack of PDFs, even if it’s only to read the annotations. The key information is also more easily accessible.

Your point about mastery is the most important, benefit though. Grappling with those annotations and fitting them within my knowledge scheme, does help me to understand the concept more thoroughly and retain it better.


My original post that you linked was specific to note-taking, but in essence your concern is just as applicable too in my own workflow. I struggled to find a system that allows the collecting of various media, not just text. I think I have settled on DEVONThink as the database. I have DTTG and work exclusive on Apple devices so not much issue there. I flirted with, but it is too underdeveloped for the features I would use (and basically requires internet to be at all useful).

As I am sure you know, DEVONThink can hold any kind of media so the next dilemma as you pointed out is the notes part. I plan on just creating linked notes to these other media (though I may toy with DEVONThink’s native “notes” field) and hold them as separate files. In this way I can just reference/review/reflect on the note and not necessarily the other media.

Regarding the problem of dealing with annotations, etc, the only way I see out of this dilemma is discipline to go the next step towards creating the ‘usable’ elements of a graphical media in the form of text. As a historian this is something that is essential to my workflow. I may have 100’s of citations in a piece of writing and it is just foolish to think I can be productive if I don’t extract the usable evidence from a piece of media and then ignore the original source until necessary.

For my lecture notes (second brain) mentioned in my original post. I will be curating a kind of abridged version of my research notes with a chain of internal links back to the original source if necessary.

So in essence, its still all plain text, but with reference to the graphical media.


There is also the concept of what have been called “sidecar files”. A file with the same name as another, and with related content.

Another possibility is using @LucCogZest’s Hook app to link related files together. There is a great screencast here

Finally, an application like Curio allows importing or linking just about anything into its idea spaces, drawing links between, inserting mind maps, lists, photo albums, etc.
Tinderbox and TheBrain are also contenders in this area, as is DEVONthink (Notebooks, Typora, etc.). I suppose it all comes down to what works best for your own mental models.


+1 “Sidecar files” are essential in this respect.


I started responding to this topic, but my response got a bit long so I ended up creating a blog post about it. Drawing Diagrams in the Head and with Technology: Benefits, Cognitive Mechanisms, Artificial Intelligence, Apps, and Sleep Onset Dreaming – CogZest.

It’s a bit of a tangent about diagrammatic reasoning from a cognitive science/AI perspective. It also contains some hypotheses about why note-taking in general (and graphical note-taking in particular) is difficult and what can be done about it. Some of it has to do with Hook.

One of the suggestions is to draw diagrams with iPad + Apple pencil, get the URL (through Hook or other means), and store the URL wherever you might want to refer to the diagram.

I personally use iPad Pro and Apple Pencil as an adjunct to my mac (I know some people prefer to rely more or exclusively on iPad)

The author of Zettlr has created a video that provides an introduction, and addresses storing text, video, images, and other artifacts in a zettelkasten system.


I agree with those above (such as @NiranS and @JohnAtl) who recommended linking to diagrams from a text file and/or including the diagrams as “sidecar files” with the text file.

And I would add, though perhaps it could go without saying, that by including diagrams in the filesystem in this way, you can use whatever diagramming tool is most appropriate for the type of diagram you need. I use any one of a number of apps depending on the type of diagram I need, such as Adobe Illustrator, OmniGraffle, Scapple, or a programming language such as PGF/TikZ: for very complex network graph diagrams, using a programming language is the only option, and when the diagram is generated by a programming language you’ll have the source code as a sidecar file along with the graphic file. Sometimes I finish a diagram in Adobe Illustrator that was started elsewhere.

All of this echoes the wisdom of using 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.”


In this video, he started talking about relational databases, and I said to myself: “What? Most people should be thinking about their note system as a graph database, not a relational database!” This continued to bother me until finally he said: But what you really need is a graph database! “Yes, exactly!” I said to myself, relieved.

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I’m curious. What is the difference?

@drfierce, I don’t think I could explain it better than the Wikipedia article Graph database, which says: “Graph databases are part of the NoSQL databases created to address the limitations of the existing relational databases. While the graph model explicitly lays out the dependencies between nodes of data, the relational model and other NoSQL database models link the data by implicit connections. […] The underlying storage mechanism of graph databases can vary. Some depend on a relational engine and ‘store’ the graph data in a table (although a table is a logical element, therefore this approach imposes another level of abstraction between the graph database, the graph database management system and the physical devices where the data is actually stored). Others use a key-value store or document-oriented database for storage, making them inherently NoSQL structures. […] Retrieving data from a graph database requires a query language other than SQL, which was designed for the manipulation of data in a relational system and therefore cannot ‘elegantly’ handle traversing a graph.”

One of the key parts here in relation to the Zettelkasten video above is that a “pure” graph database, unlike a relational database, does not rely on tables to establish connections between data. So when I said “most people should be thinking about their note system as a graph database, not a relational database”, I meant that even if a person is not really using a graph database (I don’t), the idea of a graph database is a more appropriate abstraction for a typical note system than the idea of a relational database. (I could be wrong, but that’s what was going through my head when I watched the video, which eventually confirmed what I was thinking.)

For more detail, see the lengthy section of the article titled In comparison: relational databases.


A graph database:
Edit: the strings represent relationships. The strings/connections can mean “had dinner here” or “met this person”, etc.

vs. a relational database:


I had forgotten about this when I was watching the video, but I suddenly remembered that my understanding of this comes from personal experience: At one point in my life, when I was just beginning to try to bring some order to my personal knowledge management, I tried building (what I later realized was) a personal knowledge base in FileMaker Pro, a relational database. Now, FileMaker Pro is great for some kinds of data, but I quickly found that it didn’t work well for what was becoming a Zettelkasten-like system, and I abandoned it, eventually finding my way to something like a “file system infobase manager”.

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There are several zettelkasten posts here on the forum, so just tacking this onto what seems to be the most recent. Christian Tietze is documenting his process of processing the book Range by David Epstein with a series of videos. It’s always nice to look over someone’s shoulder and see how they do things.