Zotero citations in Markdown - publishing to ePub or PDF

Mostly notes to myself - I hope you find them useful.

So, you want to write your dissertation or thesis in Markdown. But how do you manage all your citations?

  1. Install Zotero
  2. Install the Better BibTex plugin
  3. Restart Zotero. The BBT plugin will launch a configuration screen - use it to set your preferences
  4. Install VS Code (or VS Codium)
  5. Install the VS Code Zotero plugin

Now, when you want to enter a citation in Markdown, the combined plugins will generate something like this:

## Abstract

Space is really big @adamsHitchhiker1979

That @adamsHitchhiker1979 is the citation.

Formatting citations

You want to export your Markdown to something like ePub or PDF with nicely formatted citations like (Adams, 1979)

Use Pandoc!

  1. Install Pandoc
  2. In Zotero, use File → Export Library. Export in Better BibTex format as test.bib.

Add the following configuration section to the top of your Markdown file:

bibliography: test.bib

Run the following command:

pandoc --citeproc test.md -o test.epub

Hey presto! You now have a nicely formatted ePub with all the citations in your preferred format, and the bibliography at the end.

Format the citations better

The citations don't look the way I want them to!

  1. Download your preferred Citation Style from Zotero, save it as whatever.csl
  2. Add the following into your Markdown file's configuration section csl: whatever.csl
  3. Important Make sure that your citations are wrapped in [ and ] otherwise Pandoc will mess things up. See the Pandoc Citations Extension for more details.

Your Markdown should look something like this:

bibliography: test.bib
csl: whatever.csl
link-citations: true

# Intro

Computers are complicated [@verletComputerExperimentsClassical1967].

Then run pandoc --citeproc test.md -o test.epub - you can change the file type to html, pdf, or anything else your system supports.

Make it look even nicer

This is the boilerplate that I use.

bibliography: test.bib
csl: whatever.csl
link-citations: true
reference-section-title: References
title: My brilliant title

# Intro

Computers are complicated [@verletComputerExperimentsClassical1967].

## Something

More info [@smithEvolutionInnovationCapability2017]

<div id="refs">
## References

## The End

That gives you a title, ensures that all in-text citations link down to the references, and puts the references somewhere other than the end. Here's the HTML it produces using pandoc --citeproc test.md -o bib.html :

<h1 id="intro">Intro</h1>
<p>Computers are complicated <span class="citation" data-cites="verletComputerExperimentsClassical1967">(<a
         href="#ref-verletComputerExperimentsClassical1967" role="doc-biblioref">Verlet, 1967</a>)</span>.</p>
<h2 id="something">Something</h2>
<p>More info <span class="citation" data-cites="smithEvolutionInnovationCapability2017">(<a
         href="#ref-smithEvolutionInnovationCapability2017" role="doc-biblioref">Smith <em>et al.</em>, 2017</a>)</span>
<div id="refs" class="references csl-bib-body" role="doc-bibliography">
   <h2 id="references">References</h2>
   <div id="ref-smithEvolutionInnovationCapability2017" class="csl-entry" role="doc-biblioentry">
      Smith, C. <em>et al.</em> (2017) <span>‘The <span>Evolution</span> of an
         <span>Innovation Capability</span>’</span>, <em>Research-Technology
         Management</em>, 60(2), pp. 26–35. Available at: <a
   <div id="ref-verletComputerExperimentsClassical1967" class="csl-entry" role="doc-biblioentry">
      Verlet, L. (1967) <span>‘Computer "<span>Experiments</span>" on
         <span>Classical Fluids</span>. <span>I</span>. <span>Thermodynamical
            Properties</span> of <span>Lennard-Jones Molecules</span>’</span>,
      <em>Physical Review</em>, 159(1), pp. 98–103. Available at: <a
<h2 id="the-end">The End</h2>

If that was useful to you - or if you think you know a better way - please drop a comment in the box.

2 thoughts on “Zotero citations in Markdown - publishing to ePub or PDF

  1. @Edent I recently started using Obsidian. It works from a directory of .md files, each a note, and [[links]] in the notes form a graph of the connections between notes. References are just another note. I haven't dealt with the presentation layer yet. It's not perfect but it's the best thing I've found.

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