How I use it

Back when I was using Evernote, I had one notebook per source I read and its first note was a sort of bibliographical card, with basic information so I remembered what it was a long time later (it also forced me to check the outline of a paper, for example, and get more familiar with it before reading it). Sometimes, when a source A cited another source B I had already taken notes from, I would link the citation in notebook A to the bibliographical card of B. Setting this up required me to copy the information from Zotero, and I found it sad that it wasn’t really connected to Zotero itself.

With Obsidian, inside my research vault, I have a folder for “Reading notes”, where I plan to add folders for different sources (and import them from Evernote, too). It turns out that one of the citation plugin’s main features, the literature note, is precisely an automatic version of my beloved bibliographical card!

As an example, let’s say I want to add a folder for notes on Koptjevskaja-Tamm and Sahlgren’s (2014) paper. First, I press Ctrl+Shift+E and select the right entry (Figure 4).

Figure 4: Select entry from citation plugin.

This creates literature note in my “Reading notes” folder, like the one shown in Figure 5:

Figure 5: Example of literature note.

The main bibliographical information is in the Yaml² (but need not be), and then there is a hyperlink that shows the citation key (which, preceded by a @, is also the name of the note) and takes you to the Zotero entry: if I click on it, it goes to Zotero and highlights that reference.

I will later add the abstract, the outline of the paper and some comments on why I’m reading it. I also manually create the “Koptjevskaja-Tamm & Sahlgren (2014)” folder to add my new literature note and, later, other notes I might want to make.

Because the name of the note follows your chosen citation key pattern, you can easily use it to reference the source as well as the bibliographical data. So my current (new) practice is to add all references (that is, when I take notes from a source that is citing another source I might be interested in) in the format of internal notes.

For example, suppose I’m taking notes for Koptjevskaja-Tamm & Sahlgren (2014) and it references Lenci (2018). I could write it as [[@lenci_2018]], i.e. an internal link to the literature note that I could create for that second source. Even if I have not created the note yet, Obsidian lets me create the link, which means that (i) whenever I create the note it will be already linked and (ii) notes that cite the same source will be linked in the note network. Figure 6 shows a bit of my network of notes: there is no literature note for @curran_2004 yet, but it is referenced in two notes and thus connects them.

Figure 6: Snippet of network linked by a note that does not exist yet.

The easy citation key pattern means that I can guess what the reference should look like, but if there is a chance that it actually ends in a, b, etc., I can also use the plugin’s citation tool. I haven’t created a hotkey for it yet, so I have to go to Obsidian’s command palette and choose Citations: Insert Markdown citation (see Figure 7), which takes me to a menu of all my references again.

Figure 7: Choosing “insert citation” from the command palette.

The plugin allows you two kinds of citation —you access the primary one by pressing Enter and the secondary one with Shift+Enter. By default, this will insert something like [@lenci_2018], i.e. the pandoc format used by R Markdown. But, as I will show later, you can customize it to return [[@lenci_2018]], and therefore it becomes a link that you know for sure will take you to a(n eventual) literature note for that source. You can even customize it to return [@lenci_2018](zotero://select/items/@lenci_2018), that is, the Zotero entry in your Desktop app!³

As a plus, you can then copy the texts with references to your R Markdown files to create nice articles with perfect citations, just by replacing [[ with [ and ]] with ].

Customize the plugin

For a better, smoother, more tailored experience with the citation plugin, you can customize it in a few ways. I will show here what it looks like for me.

In the Settings of Obsidian and the section for the Citation plugin, you first have a few configuration items to take care of (Figure 8).

Figure 8: Customizing your citation plugin: basics.

Citation database format

I use BibLaTex (as opposed to JSON) format for my entries, which I described above (as BibTex).

Citation database path

I have exported my full Zotero library as a Library.bib file, which is stored at the top level of my vault⁴. In a previous version of this post I said:

If you make changes to your library, you have to export it again, but then Obsidian automatically refreshes.

But, it turns out, Better BibTex offers you the option of keeping track of your exported library/collection in Zotero, so that every time you modify it the file is automatically updated.

Figure 9: Keep track of the exported file.

Literature note folder

When I create a literature note, it’s automatically saved within the folder “Reading notes” (and then I move it to the folder of that source).

Under the basic configuration settings there are some instructions on how to deal with the following customization sections (Figure 10). You will write templates with variables between double curly braces, which means that they will be replaced with the matching information for the reference you cite. In other words, once you select the reference with citation key montes_2021, all the variables here that say {{citekey}} will be replaced by montes_2021.

Figure 10: Customizing the literature note.

Given those instructions, the title of my literature notes starts with a @ followed by the citation key (variable: {{citekey}}, example value: montes_2021). The initial information will be determined by the values in that template: a yaml will be created adding the values of {{title}} (the title of the referenced work), {{authorString}} (the names of the authors), {{year}} (the publication date) and {{page}} (the number of pages or the pages range), and then the body will include the hyperlink to the Zotero entry and, if available, the abstract.

---
title: {{title}}
authors: {{authorString}}
year: {{year}}
page(s): {{page}}
---
[{{citekey}}]({{zoteroSelectURI}})

{{abstract}}

The same knowledge can be used with the last section of the customization (Figure 11), which relates to the citation templates.

Figure 11: Customize citation.

As I mentioned before, you can have a primary and a secondary citation: when you ask for the citation in the command palette and it shows you the possible entries, Enter prints the primary citation and Shift+Enter prints the secondary one. In the images above, I designed the primary citation to print the hyperlink to the Zotero entry, and the secondary one to print the reference to the literature note [[@{{citekey}}]], e.g. [[@montes_2021]].

Finally, I would like to point out that I’ve been working with both Markdown and Better BibTex for a while, so if you haven’t, this can look like a lot to take. I hope you can find the time to experiment with this (or at least copy what I did, it might work for you!) and it helps your note taking, bibliography management and general levels of fun and stress!