When working on a large, long-term project (like the book I’m currently writing), I need a system for storing, organizing, and referencing ideas and resources. Although I’ve done this on paper in the past, I’m currently experimenting with a mostly digital workflow, and today I thought I’d share a little of what that looks like. The twin hearts of my current set-up are Zotero, where I store and organize journal articles, and Obsidian, where I keep and cross-link my annotations and notes.
Before I jump in, a word of warning: this post is not a tutorial on how to set up an identical system to mine. If you’re looking to do that, I set up the workflow using this wonderful post. I’m also not writing this to say that you should use a system like mine. I’m simply showing where I am in my current note-taking evolution in the hopes that seeing inside the process will be helpful for others.
With those caveats noted, let’s jump in.
Collection and Annotation – Zotero
As I go about my daily tasks, I often come across journal articles that are relevant to upcoming chapters in my book. When I do, I use my Zotero browser extension to save them into Zotero subfolders for different topics I plan to cover. When I have some quiet time — or what passes for it — I return to Zotero and pick a paper there to read.
For years, I’ve avoided annotating PDFs digitally because that information was typically locked into a single program’s format. But as of Zotero 6, their built-in annotation tools also come with the ability to export annotations and notes into the plain-text files using Markdown notation. Since this gives me access to my notes in simple .txt files (if I so choose), it helps alleviate my issues with getting locked into proprietary file formats.
As I read, I highlight passages with important information and I add notes in my own words that interpret those highlights and their relevance to my work. Sometimes I have commentary on the authors’ arguments. Other times I’m making a note of different ideas or references that this reminds me of. Basically, I try to give my future self enough information in the note that I understand why I thought this passage was worth saving in the first place.
It’s important to note that I try to keep my highlights relatively sparse in a document. If I highlight too much text, it’s overwhelming when I come back and try to parse it all. So I tend to focus on the main ideas of the article, experimental details I may need to quote, and the implications of the paper for my own work.
Once I’ve annotated the full document, I’m ready to pull those notes into Obsidian.
Building Notes from Annotations – Obsidian
I’ve been experimenting with Obsidian — a program that allows additional functionality with plain-text files like cross-linking — for about a year now. Although I’ve toyed with the idea of a formal Zettelkasten or other note-taking method, my current system is homegrown, with touches of Zettelkasten, BASB, and LYT thrown in somewhat haphazardly. Rather than adopting a whole methodology, I’ve focused on finding what note-taking method works for me, and, for now, part of that is making a literature note out of my paper annotations.
Using Obsidian’s Zotero Integration plug-in (again, using the set-up described here), I get a starting note that has biographical information for the original paper as well as all of my annotated passages and notes dumped together into it. Although it has all my raw data, I prefer my notes to display a little more neatly, so I spend some time after importing to process the note into a format I like.
Here’s what a freshly processed note looks like, with some added annotations to clarify each section:
I clean up any formatting issues (Obsidian understands MathJax so I can even make equations I’ve highlighted look right) with the annotations and offset them in blockquotes. I add my own summarizing statement in front of each quote, and I’ll tweak any additional notes I wrote to come after the quote. Sometimes I use these notes to elaborate on or remind myself of certain technical terms the paper uses. Sometimes I use them to link to other specific ideas (e.g., “This reminds me of “so-and-so’s experiment on…”) With Obsidian, I can easily drop a link to my note on the other paper using double brackets, making that older note a simple click away when I come back to this one later.
Since I’m collecting these papers with a specific chapter of my book in mind, once I’m done processing the note, I add it to my topic note, along with a one-sentence summary of the paper:
Whenever I’m ready to start drafting my chapter, this note will be my first stop. It tells me which papers I’ve read and what their main ideas were. And, if I need more information — or even to access the original paper again — it gives me a convenient trail of breadcrumbs I can follow back to the source. But, importantly, I won’t have to completely re-read the paper because I’ve already done the hard work of telling my future self what’s important to me about the paper. In most cases, that will be enough. If I have a question or need a detail that my notes don’t answer, I can go back to the original.
Using My Notes Later On
Although I’ve illustrated my system here with a journal article, I keep similar notes for books that I’ve read, and already I’ve found the results invaluable. Instead of feeling like I need to go back and re-read an entire book, I can skim through my literature note and see what was important to me. With these notes, I also add a layer of highlighting that draws my eyes to the key ideas. (This is borrowed from Tiago Forte’s progressive summarization technique.) Especially in my long notes, this technique helps me keep the text easily skimmable so that I can zero in on the topic I want. Here’s a look at my note on Jack Hart’s Storycraft:
Using a little CSS and some hotkeys, I’ve set it up so that I can quickly and easily bold, highlight, and color passages that stand out to me. To help me distinguish others’ words and ideas from my own, I use two different colors: blue for the original author and orange for my own comments.
I don’t typically add in these highlights when I first process a note; they’re something that I add later when I come back to use a note. I find that these highlights add an extra layer of usability to my notes, and it’s always a joy to come back to a note that has these extra features. They make it much easier to quickly find what I need in any given note.
Once upon a time, when I sat down to write, it was always with freshly-read papers in my mind. But life’s distractions don’t allow anymore for that kind of pre-writing cram session. Instead I squeeze productive work into whatever corners of my schedule that I can find. So in this season of life, being able to pick up where I left off is invaluable. Taking, processing, and tweaking literature notes is one way that I enable that workflow. This system helps me quickly find the relevant paper, remind myself of its importance, and seek out more details if I need them. It’s not a perfect solution, and I expect it to evolve further over time, but I hope it will be a process of refinement rather than revolution.
What systems do you use to manage the constant influx of knowledge? Do you have any helpful tips and tricks of your own? Sound off in the comments below.
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(Image credit: S. Graham)