Introduction

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

• A reference document combined with Pandoc saves time layouting.
• The BetterBibTeX Plugin enables the use of citekeys which are basically unique and unambiguous identifiers that link notes to the reference library. Using the Obsidian Citations Plugin by Jon Gauthier, citations can be inserted into Obsidian during note-taking and writing. (A smart renaming pattern is to use citekeys, as the PDFs are linked to the reference library entry via its filename – it's hard to get more future-proof than with filenames.)

However, there are also some disadvantages:

• The most common method of using Pandoc is it's Command Line Interface ("CLI"), which is daunting even to some tech-savvy people.