Zotero to Obsidian

Getting Zotero and Obsidian really working well together

Introduction

This post describes my process of getting two excellent applications (Zotero and Obsidian) working together in my writing workflow. The challange is balancing how much time I spend on work vs. how much time I spend on my workflow, but thats a topic for another post [[Research Procrastination]]. The workflow in a nutshell involves getting Zotero set up with a few plugins and then setting up Obsidian to be able to pull in the annotations from Zotero. The result is well formatted notes in Obsidian linked to your other research while also maintaining links back to the orignal text in Zotero.

Finding Zotero (..or making new friends over 40 )

Having used an array of reference managers and literature databases in the past, I have settled on Zotero as my reference manager of choice for a number of reasons. The number one reason is that it does its job of managing and inserting references into academic texts extremely well. The other package that I have used previously, which performed very well in this capacity was Mendeley, but its whole demeanour has changed in recent years since its tighter integration with Elsiver and I began to become very fearful of not having a local copy of my database which I could back up myself. I really enjoyed using Papers on the Mac but then I had to use PC’s as well and that got to be a pain and they have now moved to a subscription model. Its well priced and lovely to use if you stay in the Apple ecosystem. I’ve also used Endnote as its supported by my institution. After the user friendly goodness that was Papers, it was very hard to see the value added in Endnote. In the search for an open source solution to reference management I discovered Zotero, which, in addition to being open source (free as in speech and free as in beer) also provides the best reading and annotation functionality I have come across in these applications. I pay $20 a year to benefit from the online sync and storage but this is not required to use the application on your main computer and you can use other sync services. I have migrated across and have everything in there, even dating back to my orthopaedic days.

Introducing Obsidian (…or “Down, down, down. Would the fall never come to an end? “)

What is obsidian
Out of the box its a markdown editor with an ability to map the interconnections between your notes. Built by a small team to plug a gap in their own note-taking requirements.

• Where has it come from Obsidian was created by a team of software engineers and designers who wanted a powerful note-taking tool for their own work. They built it using Electron, a framework for creating desktop applications using web technologies. The goal was to make a flexible app that could handle large numbers of interconnected notes, using plain text files (markdown) and folders.
• Earlier note-taking apps like Tomboy and Gnote used basic linking between notes, but did not have the graphical network views and advanced features of Obsidian. Obsidian allows you to make both internal links between your notes, and external links to websites or other resources.
• Obsidian utilizes Markdown, a simple text formatting syntax, along with YAML front matter for templates and metadata. It has a robust system of hashtags, links and backlinks to tie notes together. There is also an active plugin community that adds additional functionality to the app. Combined, these features make Obsidian a very compelling tool for managing knowledge and writing long-form content.
• While the Obsidian app is free to download and use, the source code is not openly available. The developers aim to build a sustainable business model around the software, while keeping the core features free for personal use. This approach allows quick updates to the app based on user feedback, without the complications of open source licensing and contributions. Overall, Obsidian provides a lot of value for the price (free!) and is worth considering as a power note-taking tool, especially if you want to write or organize long, complex documents. The unique graph view and focus on building connections between your notes can lead to new insights and ideas. Combined with a reference manager like Zotero, Obsidian is a great addition to any researchers toolkit.

A Recipe for Happiness

Lower your expectations is apparently the real answer to that quandary, but I digress.
My recipe for Zotero Obsidian based happiness is as follows.

Install the Zotero plugin and set up the folders you want to save into.
I then use this template as the Zotero import (posted as pdf so Jykell dosent get over enthuastic and try to render it) . This produces a nicely formatted result with the highlighted text, clipped images and annotations, with links back to the right spot in the paper in the Zotero database. Magic. Link those notes to your other thoughts and notes and you get to the beginnings of a literature review. As with all these productivity tools the trick is to not get distracted by the tool to the extent that you forget to do some actual work .