1 Getting started
It’s been a while since I have been trying to find various productivity software to prepare myself for my future Ph.D. journey. One of those tasks which I wanted to automate was in organizing my scientific literature collection. The answer to organizing and annotating the literature was met by two software; Zotero and Notion. Zotero is a free-to-use reference manager that can organize your literature collection with ease. Notion, on the other hand, is a productivity software that can be used as a workspace manager, task manager, and many other things. I have written a guide on how one can use Zotero and Notion to build a literature tracker.
Now that the organization part is taken care of, I was in search of software that can help me take summary notes on the literature that I am studying. Now I can write notes and embed them into the .pdf file using Zotero itself or use Notion to create notes using the literature database which is synced with the Zotero libraries. Both these methods work, but I wanted something versatile. And that’s what brought me to Obsidian, an open-source, free-to-use, note-taking software that uses the Markdown language at its core. In this blog post, I will show you how I use Obsidian to take literature notes.
2 Using Obsidian with Zotero
Before we begin, the picture given below shows my Obsidian interface. The interface is broken down into different panels, where each panel shows specific info.
Now the primary goal for me in using Obsidian is to write summary notes of the papers that I am reading, but at the same time, I can also so use it as a research diary and as a general note-taking software to write my thoughts and ideas. One good thing about Obsidian is that you don’t need an active internet connection to use it and also the markdown files that you will be making will be saved locally. So let us get started!
2.1 Setting up Obsidian
We will first see how to create the interface that we saw earlier. For that let us first install Obsidian.
- Installing Obsidian is very easy. Just visit their official website and download the version suited for your operating system. I assume that you already have Zotero on your computer. If not, then please visit here and download the appropriate version for your system. Now that we have both Obsidian and Zotero, let us get started.
When you first open Obsidian, it will ask you to create a vault as shown above. The vault is a folder location that will contain all the markdown files you will be creating. Now instead of doing everything from scratch, for convenience, I will be sharing my vault template folder so that you can get started quickly. The folder will also contain the necessary plugins and configurations to jump-start your Obsidian journey.
Download the folder as a zip file from here.
Extract the zip file and open the folder in Obsidian using ‘Open folder as vault’ as shown in ?@fig-start. If done properly, then you will get the following interface as shown in the image below.
I use the following plugins which are not owned or made by me. The credits go to the plugin developers. You can learn more about the plugins by following their GitHub repo links.
2.2 Setting up Zotero
Now before we proceed, let us configure Zotero. We will use Zotero to create a BibTeX file from a library. Now, this .bib file will contain all the metadata of the literature present in that library. But we won’t be making a normal .bib file, instead, we will use a plugin called ‘Better BibTeX for Zotero’ to make the .bib file, which features an auto-update feature. What it means is that, as you add more literature to your Zotero library, the .bib file will automatically update. Pretty cool right?
Download the ‘Better BibTeX for Zotero’ plugin from here. Hover your cursor to
zotero-better-bibtex-6.7.36.xpi, then right-click and select ‘Save link as’ to download the addon.Then open up Zotero and navigate to Tools -> Add-ons. Then go to the setting options by clicking on the gear icon and then select ‘Install add-on from file’. Browse to the location where your file was downloaded and then install the addon.
Let us now configure the plugin. Select Edit -> Preferences -> Better BibTex. In the ‘Citation key format’ section replace the existing text with the following:
authEtal2+year.
This will change the citation key to the ‘author name + year’ format which is much more useful and easy to understand than the default citation key format. You can visit here to learn more about how to customize your citation key format.
Finally, select the folder which you want to make a .bib file for. If you want to access all the literature files from the Zotero library, then export the .bib file from ‘My library’.
Right-click on ‘My library’ and then click on ‘Export library’. A small window will pop up, select ‘Better BibLaTeX’ from the format option. Check the ‘Keep updated’ option, this will auto-update the .bib file when you add new files to the Zotero library. You can also check the ‘Export notes’ option if you want to export the highlights and annotations that you have made on the .pdf files using Zotero.
Save your .bib file in a location of your choice. Then copy the full path (file location) to the .bib file. We will be needing this shortly.
2.3 Configuring the plugins
As you are using my template, you don’t have to individually download the plugins which I am using. But you do need to configure a few settings (only two configurations). Let us configure the ‘Citations’ plugin first.
- Go to the setting page in Obsidian. Then under ‘Community plugins’ select the ‘Citations’ plugin. Then in the ‘Citation database path’ paste your .bib file path.
As an example my .bib file location is the following; /home/jewel/Downloads/Example.bib
The syntax of the citations template that I am using is the following;
---
title: "{{title}}"
authors: {{authorString}}
year: {{year}}
citekey: {{citekey}}
---
>[!title]
{{title}}
>[!year]
{{year}}
>[!author]
{{authorString}}
------------------------------------
URL: {{URL}}
Zotero link: [@{{citekey}}]({{zoteroSelectURI}})
tags::
------------------------------------
### Research question
1.
### Findings
1.
### Discussion
1.
### Methodology
1.
### Remarks
1.
You can visit the official GitHub repo of the Citations plugin or read the instructions shown in the plugin window in Obsidian to learn more about how to customize the template.
You also need to configure the ‘Pandoc Reference List’ plugin. To use this plugin you would need the pandoc package installed on your computer. Most operating systems have it pre-installed and if you don’t have it then please visit here for info on how to install the package. For Linux users, you can install ‘pandoc’ using your package manager by searching.
- Head on to the ‘Pandoc Reference List’ plugin under the ‘Community plugins’ section. In ‘Path to Bibliography File’ section, paste the same path location as before (i.e. the location of your .bib file).
2.4 Using the citation plugin
To access the plugin in the note window, press Ctrl+P to open up the commands menu. Type ‘Citations’ and view the different options. For quick access, you can press Ctrl+Shift+E instead and browse through your library collection and search for the literature that you want to reference.
By selecting a literature entry, a markdown file (.md file) will be automatically created in your ‘Literature_collection’ folder. You can open these markdown files and then make the necessary edits. I use them to write the summary and my understanding of that paper in the .md file.
I have also made a literature table using the ‘Dataview’ plugin. You can configure the source code of the table to suit your needs.
The source code is as follows;
```dataview
table title, authors, year, tags
from "Literature_collection"
sort year desc
```The syntax picks up .yaml headers like title, authors, year and tags, all of which have been pre configured in the literature .md files using the Citations plugin template that we saw before. You can learn more about how to configure the table here.
3 Conlusion
I have just started out using Obsidian and so far I have had an amazing experience. There are a lot of community plugins available and I get easily overwhelmed by them. You can browse the plugins collection and see what fits your interests. I hope you find this guide helpful and let me know in the comments about your experience with Obsidian.
4 Plugin credits
I use the following plugins in my workflow. You can learn more about these plugins in the links given below.
- Obsidian Admonition
- Autocomplete Obsidian Plugin
- Better Word Count
- obsidian-calendar-plugin
- obsidian-citation-plugin
- cMenu Plugin
- Obsidian Dataview
- Obsidian Icon Folder
- Obsidian Pandoc Reference List
Reuse
Citation
@online{johnson2022,
author = {Johnson, Jewel},
title = {Using {Obsidian} as a Note-Taking Software for Academic
Purposes},
date = {2022-11-08},
url = {https://sciquest.netlify.app//posts/obsidian_zotero},
langid = {en}
}