A Stack of Text Files + Obsidian Interface = Personal Knowledge Management System

(See my previous post about Obsidian here. This post is written for my students, except for the bit at the end)

In recent years, I’ve found that a lot of my research materials are all online. Everything I read, everything I study. I use Zotero to handle bibliography and to push pdfs to an iPad with zotfile; then I annotate as I read on the device, and eventually, retrieve the annotations back into Zotero.

I read on a browser on my work computer too; I use hypothes.is with a private group where I’m the only member to annotate websites and pdfs in the browser when I can’t be bothered to send them to the ipad.

I use a notebook where I scribble out ideas and page numbers.

All of this material is scattered around my devices. I’ve long admired the work of Caleb McDaniel, and his open notebook history. His research lives online, in a kind of wiki. Links between ideas and observations can be made that way and eventually, ideas can emerge out of the notes themselves by virtue of the way they’re connected. This is the idea behind what is called the Zettelkasten Method (‘slip box’, where each idea, each observation is kept on a discrete slip of paper numbered in such a way that connections can be formed):

A Zettelkasten is a personal tool for thinking and writing. It has hypertextual features to make a web of thought possible. The difference to other systems is that you create a web of thoughts instead of notes of arbitrary size and form, and emphasize connection, not a collection.

On a computer, such a thing can be created out of a folder of simple text files. Everything I observe, every idea that I have: one idea, one file. Then I use the free ‘second brain’ software, Obsidian to sit ‘on top’ of that stack of files to enable easy linking and discoverability. Obsidian helps you identify connections, backlinks and outgoing links, between your notes. It visualizes them as a graph too, which can be helpful. Obsidian works as a personal knowledge base; seeing your notes develop and begining to interlink – and being able to search those patterns – supercharges your note taking abilities and the value of your reading. With time, you’ll start to see connections and patterns in your thoughts. You’re building up a personal knowledge base that becomes more valuable the more you use it. It can be extended with all sorts of plugins, written in javascript (since Obsidian is an electron app). Some of the plugins I use are Dataview (which lets you create new notes that query other notes’ metadata – keeping track of all notes relevant to a particular project, for instance) and Journey, which finds the shortest path between two notes (and you can then copy that path into a new note that embeds the contents of the notes along the journey: boom, instant article outline!)

I haven’t been playing with Obsidian for too long, but I do have a folder with over 400 separate markdown notes in it, the legacy of previous experiments with zettel-based systems. But so far, Obsidian seems like a winner. When I get an idea, I search my vault for relevant notes, and then it is easy to embed them into a new document (type [[ and start writing; any existing notes with that tile are found; close with ]]. Then put a ! in front of it: the note is embedded. Add a ^ after the note title, and you can embed specific blocks or paragraphs from the source note). I write around the existing notes, and then export to word for final polishing, citations (copy and paste; or install the pandoc plugin). This accelerates my writing considerably, and helps me pull my research together into coherent form. (Of course, since I’ve developed these notes across several different systems in my perennial search for the notetaking system to rule them all, my metadata usage isn’t consistent, which hampers things a bit).

Obsidian calls a folder with markdown files in it a ‘vault’. This vault can live in your icloud folder, your gdrive folder, your dropbox folder. You can initialize it with Git and push copies to a private git repo. Since the files are locally store, the whole thing is very fast, and you’re not locked in to using Obsidian if you decide something else would be better. I’ve started making a number of what I am calling ‘starter’ vaults for my students, to use in my upcoming courses. Since my courses this year are mostly methods-based, I want the students to use Obsidian as a kind of empty lab notebook. My starter vaults are configured with a few basic templates, some basic important course information, and a script for retrieving their Hypothesis annotations:

And for the ambitious student, a vault configured with every plugin and template I could find that I figured would be helpful for a student at https://github.com/shawngraham/obsidian-student-starter-vault

These include:

  • ocr templater extracts text from images and inserts into a new note
  • extract notes from hypothesis
  • citations from zotero bib
  • with mdnotes installed in zotero, you can export your zotero notes to this vault
  • with refactor commands, you can break big notes into atomic notes
  • with the ‘related’ templater, you can use text analysis to find notes that are similar, to enable linking
  • open the backlink pane, and use backlinks and outgoing links to find potential connections with other notes (compares the text of the note to the title of notes, finding matching strings for potential linking)
  • use the journey plugin to find paths through the vault, chains of ideas; these chains can be inserted into new notes
  • use transclusion (embedding) to create long overview notes that pull your ideas/observations from atomic notes into something that can become the core for a paper or article
  • queries to see how long you’ve got left for a writing project, and to see which resources you’ve used for what project
  • kanban boards for project management

Finally, I am also using an Obsidian vault configured with Dataview to try to improve my project management. I have a few research projects with several moving parts, plus responsibilities coordinating a graduate programme and a minor programme. This vault looks like this:

On the left, the ‘preview’ (non markdown) version of the index note that links out to several project notes. At the bottom is a table that pulls together notes on each of my graduate students with things that I need to keep track of. In the right hand pane, another note is open, showing the markdown code block that invokes the dataview plugin. The plugin searches through the metadata of each note about my individual students, pulling out those students who are formally working on my various projects.

Anyway, so far, so good. Give obsidian.md a play! Download it, and open the demo vault to get a sense of whether or not this approach to note-keeping works for you.