Research methods and tools for a Humanities PhD: Zettelkasten, Obsidian, Zotero, and Pandoc

My main approach to qualitative research is inspired by Niklas Luhman’s Zettelkasten method—my Zettelkasten is named “House of Pomegranates”, after my favorite Oscar Wilde short story collection. Very briefly, the Zettelkasten, for me, is a method that has encouraged me to turn the highlights and notes I take during reading (“fleeting notes”) into critical summaries (“literature notes”), which slowly build up concrete ideas (“permanent notes”), which, again, for the basis for a manuscript (i.e. my dissertation manuscript or other academic texts. Not everything I read and take notes on gets turned into a full-fledged literature note; not every literature results in the creation of new permanent notes; not every permanent note gets used in my manuscript. The goal is not to accumulate knowledge per se, but to have a personal wiki that reflects my research interests and the contexts I need in order to produce my doctoral dissertation and other academic texts. That said, I do always try to get the most out of my readings. Although there are many excellent sources on the Zettelkasten method, I can particularly recommend Sönke Ahrens’ book How to Take Smart Notes. LeanAnki’s Beginner’s Guide is also an excellent place to start.

Obsidian is my note-taking software of choice, where I write my literature and permanent notes as well as my dissertation manuscript. I use Obsidian because it uses plain text (Markdown), stores my notes locally, works incredibly fast, and allows connecting notes (as well as paragraphs and sections) and embed them (![File^ or ![File#) with great ease. It is a simple yet incredibly powerful tool that has helped me take a digital Zettelkasten approach to note-taking and creating knowledge (or approaching knowledge creatively). I learned about the uses of plain text writing for academic texts from this series of blog posts, and I learn about new features in Obsidian on a near-daily basis from watching YouTube videos (Brian Jenks, Obsidian Office Hours, LinkingYourThinking, and KeepProductive, i.a.). For Markdown-specific questions, I recommend the Markdown Guide.

Zotero is my reference manager: i.e. it contains all my references (with or without attachments) and corresponding metadata. I use a variety of Zotero plug-ins and features: BetterBibTex, Zotfile, Zotero import from keyboard, and Zotero Connector to manage and cite my references as well as my highlights and notes within Zotero. In addition, I use Argentum’s Mdnotes plug-in to export my notes and metadata from Zotero to Obsidian in Markdown. Although I have used Mendeley and EndNote in the past, I strongly prefer Zotero because it is open source software that is developed by an independent, non-profit organization (as opposed to Mendeley), it is free (as opposed to EndNote), and it integrates quite nicely with plain text editors. I learned how to use Zotero from these Nicholas Cifuentes-Goodbody’s tutorials. See the Zotero documentation for written instructions.

Pandoc is the document converter I use to convert my Markdown files into a properly formatted document with citations and a bibliography.  This series of posts got me introduced to the world of plain text writing and Pandoc, and Nicholas Cifuentes-Goodbody also has this very basic but excellent video on Pandoc. There’s also always the option to “Export to PDF” within Obsidian. I have done this for a couple of non-important files (that did not need to render citations). In my last post from this series, “From permanent notes to a manuscript: Pandoc“, I share my code for Pandoc conversions as well as a Keyboard Maestro macro I use to automate Pandoc conversions.

Less central to my workflow, but otherwise still invaluable, are the following apps:

  • Visual Studio Code is a code editor that I use to search-and-replace in bulk throughout my vault, a crucial function that is missing in Obsidian. I use it for a very diverse set of issues: from creating automatic backlinks, standardizing language or formatting, cleaning up imported files, etc.
  • Keyboard Maestro is automation software for macOS that I use to automate certain repetitive tasks, such as creating and formatting my most-often used typestrings and/or backlinks (e.g. ;mthp inserts *[[MOC The Happy Prince and Other Tales|The Happy Prince and Other Tales]]*, ;thp inserts *The Happy Prince and Other Tales*, and ;prince inserts "[[The Happy Prince]]", etc.). I use Keyboard Maestro for other tasks as well but this feature alone has saved me HOURS within my Obsidian Zettelkasten.
  • Numbers (macOS) is the program I use to create spreadsheets that help me keep track of a lot of information that is sprinkled across a lot of permanent notes (e.g. dates of events such as births, deaths, inventions, publications, the name, price, periodicity, and other details of the periodicals in which Wilde’s short fiction was initially published; an overview of the source’s I have read vs. those I still need to read; etc.). I use Numbers for convenience, seeing as I am on macOS. In my last post of this series, I share an example of how I use Numbers.

This is the preliminary step of my research workflow. For the rest of the series, see:

4 thoughts on “Research methods and tools for a Humanities PhD: Zettelkasten, Obsidian, Zotero, and Pandoc

  1. Thank you for share your workflow with so great references and links. After read your text, I become curious about how did Zotero 6 modify your research and writing flow. Have the new features changed your way of working?


      1. This is an important time to dedicate yourself to motherhood. When you get back to your research activities with zotero, I believe you will like the new version. Many tasks are now simpler and more integrated, especially with reading PDFs and the annotation process.


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