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

The simple Word-Zotero version

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

However, there are also some disadvantages: