In a previous post I already talked about a format I use a lot: BibTeX. I like it because you can easily convert it to other formats. In addition, you almost never really have to encode the BibTeX entries yourself: they are

• either directly downloadable from the journal webpage (“Export citation”)
• or you can get it them from the publication Digital Object Identifier (DOI). Have a look at my script doi2bib to see how easy it is.

Here is an example of such a BibTeX file:

@Article{TROUPIN2019,
  Title                    = {The AlborEX dataset: sampling of sub-mesoscale features in the Alboran Sea},
  Author                   = {Charles Troupin and Pascual, Ananda and Ruiz, Simon and Olita, Antonio and Casas, Benjamin and Margirier, Félix and Poulain, Pierre-Marie and Notarstefano, Giulio and Torner, Marc and Fernández, Juan Gabriel and Rújula, Miquel Àngel and Muñoz, Cristian and Alou, Eva and Ruiz, Inmaculada and Tovar-Sánchez, Antonio and Allen, John T. and Mahadevan, Amala and Tintoré, Joaquín},
  Journal                  = {Earth System Science Data},
  Year                     = {2019},
  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {129–145},
  Volume                   = {11},
  Doi                      = {10.5194/essd-11-129-2019},
}

Conversion tool

pandoc is a powerful tool that makes it possible to perform different format conversions, for instance from LaTeX to HTML, to pdf or to Word. Here are a few basic examples of calls:

pandoc input.tex -o output.pdf
pandoc input.md -o output2.pdf
pandoc input.md -o output3.docx

I must say I’m not a big fan of all those formats, but still, having a tool to convert from one to another is great.

Here we want to generate a Markdown from a list of references stored in a BibTeX file. In order to do so, we have to install pandoc-citeproc, as documented here.

Procedure

1. Create a file that will call the bibliography, we will call it nao_ref.md.

   ---
   bibliography: nao.bib
   nocite: '@*'
   ...
   

   Basically it says that it has to read the references from nao.bib and cite all of them.

2. Run the following command:

   pandoc -t markdown_strict --filter=pandoc-citeproc nao_ref.md -o nao.md
   

   Here it is: nao.md can now be used, for example in a presentation (well, maybe not a good idea to list references in a presentation), or in a web page. We just paste one reference of the list.

   Narayan, N., A. Paul, S. Mulitza, and M. Schulz. 2010. “Trends in
   Coastal Upwelling Intensity During the Late 20th Century.” *Ocean
   Science* 6 (3): 815–23. <https://doi.org/10.5194/os-6-815-2010>
   

Customizing

The result is a little blunt, let’s see what we can do to improve it.

Add content

We can easily edit nao_ref.md, for instance:

---
bibliography: nao.bib
nocite: '@*'
...
### North Atlantic Oscillation
Here is a list of relevant publications related to the NAO.

After running again the pandoc command, the last 2 lines we’ve added at the end of the file will be present in the MarkDown file.

Changing style

Each journal has its style concerning the bibliography (the famous bst files, if you’re using LaTeX). Here the equivalent is the so-called Citation Style Language (.csl) files. You can browse a massive list of styles and chose the one that fits.
Here we decided to go with ocean-science.csl. We add the option to the pandoc command:

pandoc -t markdown_strict --filter=pandoc-citeproc --csl ocean-science.csl nao_ref.md -o nao.md

and the resulting reference is now:

Narayan, N., Paul, A., Mulitza, S. and Schulz, M.: Trends in coastal
upwelling intensity during the late 20th century, Ocean Science, 6(3),
815–823,
doi:[10.5194/os-6-815-2010](https://doi.org/10.5194/os-6-815-2010),
2010.

Full control!

If you ever want to generate your own style, this documentation explains how to do it. Nevertheless, with the available styles, it might not be necessary.