Using Pandoc for Doing Citation and Bibliography in Markdown

Markdown is a simple formatting syntax that allows you to do common formatting with ease. Pandoc is a feature rich interpreter that helps you convert documents from one format to anther. If you are writing homework, research papers, or anything that needs citation and a bibliography, you can totally use Markdown and Pandoc to achieve that.

Below is a set of instructions that you can follow to generate a document with in-text citation and bibliography.

First, install Pandoc and the extension for creating citation (pandoc-citeproc). 

There are several ways to install Pandoc, you can choose one of them recommended on the official website. On Mac, one way is to install Homebrew, a package manager, and then use Homebrew to install Pandoc and the extension. For Windows users, please refer the official website on how to install Pandooc and extension.

Here I will show how to install Pandoc and the extension for citation through Homebrew.

After installing homebrew, you can execute the following commands in your terminal to install Pandoc and the extension.

brew install pandoc
brew install pandoc-citeproc

Second, prepare the following three files and put them in the same folder.

1. Your writing in Markdown syntax (.md).

writeup.md

2. The desirable citation style definition (.csl).

There are multiple citation styles that are used by people from various disciplines. For instance, APA is a common style recommended by the American Psychological Association (APA). You can choose APA if you do not have a preference as it is one of the most popular citation styles. You don't need to write the citation style definition by yourself, as you are very likely to find the style provided by some of the popular citation managers. For instance, Zotero provides a repository of citation styles that you can download.

writeup.csl

3. The references (e.g., .bib).

This is the file that you list all the information for the references. One of the common formats is the .bib (BibTex) format, which you can download it from Google Scholar when you find a reference. Each entry in the .bib file will look similar to the following one.

@misc{this_is_the_article_id,
...
}

Pandoc supports different formats. Here I will use .bib (BibTex) format to demonstrate how to create a bibliography.

writeup.bib

Third, insert in-text citation. 

Here is an example of how to do it. For a BibTex entry that looks like the above example, you can insert in-text citation by inserting the article_id preceded with an @ and then surround it in square brackets. For instance,

I will cite right here [@this_is_the_article_id].

Lastly, generate the output document with in-text citation and bibliography.

After you finished doing all the in-text citation, you can type the following command to generate the resulting document with in-text citations and the bibliography.

pandoc writeup.md --filter pandoc-citeproc 
--csl=writeup.csl --bibliography=writeup.bib -o writeup.pdf

That's it! You can then find your output document with in-text citation and bibliography at the end of the writeup.pdf file.

If you want the output in some other format (e.g., docx) instead of pdf, just change the file extension and Pandoc will do it for you (if suppored).

Hope this help!