by Chris Grieser

Last Update: 20. December 2021


This is an overview over a comprehensive academic workflow, from getting annotations into Obsidian to writing a publication with Pandoc citations in Obsidian as well. There has already been a detailed description of how to achieve this with Zotero and MDnotes. The workflow I describe here deals with very much the same problems, but takes a different direction. The goal of this post is, however, not to provide a step-by guide for implementing a workflow with certain apps or plugins. Rather, this post will discuss a general workflow for academic work which can be implemented with a variety of tools. Basically, the one goal of this post is not to explain how to use certain tools, but rather to explain what the tasks are you should be using software tools for. And, of course, how to structure the individual tasks in such a way that everything works with minimal friction. The other goal of this post is to provide an overview of tools that can be used to accomplish those tasks. The overall intention is to give readers the autonomy to choose their own set of tools to customize their individual workflow.

First, I will outline the Academic Workflow from Reading to Writing in general and how to how it is implemented in different workflows by the average user and by the advanced Zotero user. Then, I will briefly outline my implementation and discuss why I do not use Zotero for it.(Disclaimer: I haven't used Zotero 6.) I will end with an extensive overview of several tools (apps, plugins) that together provide comparable features.

The Academic Workflow from Reading to Writing

The generalized version

This basic academic workflow looks something like this: You find an article on a website, and save it in your reference library (i.e. reference manager). The library entries should be linked to the PDF file of the paper, from which we want to extract notes to our knowledge base (i.e. Obsidian). Ideally, we want to keep the link between library entry, knowledge base, and PDF.

Later on, you use your the knowledge base to write an article of your own. When you cite a paper you have read, you basically create a link between the Draft and the entry in your reference library. During the final compiling of finished draft, the citations are used to add the bibliography to the finished manuscript. Ideally, you also use a template to save the time of creating a new layout every time you write a paper.

The abstract version of the academic workflow from reading to writing

The abstract version of the academic workflow from reading to writing

The simple Word-Zotero version

Workflow of the "average" researcher

Workflow of the "average" researcher

However, the outlined workflow is not only a very generalized version, but quite idealized. The "average" researcher, mostly far from being power users, will often have a much simpler version. Let's imagine such a less tech-savvy academic, who still uses Microsoft Word. In addition, that person uses a reference manager (let's say Zotero), and uses the builtin plugin for Word Citations and the Zotero Browser extension, because those two tools are quite easy to use and are "officially" provided/advertised by Zotero. In their case, the workflow from reading to writing should look something like the graph to the left.

Apart from the lack of a dedicated note-taking system, quotes and information from PDFs are mostly copy-pasted, and the unorganized notes (e.g. a long list of bullet points in a separate document 🥶) will contain author and year of the reference. While this is an "implicit" link to the entry in the reference library, this is far from perfect (e.g. ambiguity when there are two papers by the same author in the same year).

Another thing to note is that the missing link between the unorganized scrawl and the PDF makes going back to the context of a quote rather tedious: our "average" researcher will open up Zotero, search for the respective entry, and then open the PDF. Also, working on multiple devices gets quite complicated since Zotero and PDFs may both for themselves sync between devices, but keeping the link between them is definitely a struggle without further plugins.

Nevertheless, this workflow does accomplish some things well: using the first-party Zotero tools, articles are easily saved and citations are easily inserted. The compiling of the final document is particularly easy, since using the Zotero-Word-workflow enables to export the draft as PDF with just a few clicks.

The Zotero-ZotFile-BetterBibTeX-MDNotes-Obsidian-Pandoc version

Now many people here and especially power users dislike Word and would prefer to write in Markdown. As (on average) technologically more adept users, they want to automate tedious tasks like copy-pasting quotes. In addition, they use have a note-taking system like Obsidian. Following the much-mentioned Zotero-ZotFile-MDNotes-Workflow and adding Pandoc, their system is more sophisticated and should look like this.

Compared to the simpler Word-Zotero-Workflow, this has many advantages:

The Zotero-MDNotes-Obsidian Workflow.
(The graph is unfortunately mirrored, since mermaid.js weighs stuff differently here.)

The Zotero-MDNotes-Obsidian Workflow. (The graph is unfortunately mirrored, since mermaid.js weighs stuff differently here.)

However, there are also some disadvantages: