Lesson 12

Citations and references

This lesson show the basics of reference databases. Learn how to build your own databases and how to use them in documents using the two major workflows available.

For bibliographic citations, while you can include reference sources directly in your document, usually you will get that information from one or more external files. Such a file is a database of references, containing the information in a processing-friendly format. Using one or more reference databases lets you re-use information and avoid manual formatting.

Reference databases

Reference databases are normally referred to as ‘BibTeX files’ and have the extension .bib. They contain one or more entries, one for each reference, and within each entry there are a series of fields. Let us look at an example.

@article{Thomas2008,
  author  = {Thomas, Christine M. and Liu, Tianbiao and Hall, Michael B.
             and Darensbourg, Marcetta Y.},
  title   = {Series of Mixed Valent {Fe(II)Fe(I)} Complexes That Model the
             {H(OX)} State of [{FeFe}]Hydrogenase: Redox Properties,
             Density-Functional Theory Investigation, and Reactivity with
             Extrinsic {CO}},
  journal = {Inorg. Chem.},
  year    = {2008},
  volume  = {47},
  number  = {15},
  pages   = {7009-7024},
  doi     = {10.1021/ic800654a},
}
@book{Graham1995,
  author    = {Ronald L. Graham and Donald E. Knuth and Oren Patashnik},
  title     = {Concrete Mathematics},
  publisher = {Addison-Wesley},
  year      = {1995},
}

This is an entry for an article and another for a book; these are by far the most common types. Each database entry type starts with @, as shown, and all of the information then sits within a brace pair.

The various fields we need are given in key-value format, apart from what is known as the ‘key’: the ‘name’ of the citation. You can use whatever you like, as it’s just a label, but above we’ve chosen to use the name of an author plus the year: this is a common approach.

Exactly which fields you need to give depends on the type of entry, but most of these are quite obvious. You might notice that in the author field, each entry is separated by and. This is essential: the format of the output needs to know which author is which. You might also notice that in the article title, some entries are in an extra set of braces; these are there to prevent any case-changing being applied.

Editing .bib files by hand is rather tedious, so most people use a dedicated editor. JabRef is widely used and cross-platform, but there are several other interfaces available. If the reference contains a DOI (Digital Object Identifier), you may want to try doi2bib to easily get the BibTeX entry. But make sure to check if the entry is correct!

Here, we will use the short example database above for our demonstrations: we have ‘saved’ it as learnlatex.bib.

Transferring information from the database

To get the information into your document there are three steps. First, use LaTeX to compile your document, which creates a file with a list of the references that your document cites. Second, run a program that takes information from the database of references, picks out the ones that you use, and puts them in order. Finally, compile your document again so that LaTeX can use that information to resolve your citations. Usually it will require at least two compilations to resolve all the references.

For the second step, there are two systems in wide use: BibTeX and Biber. Biber is only ever used with a LaTeX package called biblatex, whereas BibTeX is used with either no packages at all or with natbib.

Running a second tool as well as LaTeX is handled in different ways by different editors. For our online examples, there are some ‘behind the scenes’ scripts that do everything in one go. Your editor might have a single ‘do stuff’ button or you might have to choose to run BibTeX or Biber manually between LaTeX runs.

The format of citations and references is independent of your BibTeX database, and is set by what is known as a ‘style’. We will see that these work slightly differently in the BibTeX workflow and biblatex, but the general idea remains: we can choose how citations appear.

The BibTeX workflow with natbib

Whilst it is possible to insert citations into a LaTeX document without any packages loaded, this is rather limited. Instead, we will use the natbib package, which allows us to create different types of citation and has a lot of styles available.

The basic structure of our input is as shown in this example.

\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage{natbib}

\begin{document}
The mathematics showcase is from \citet{Graham1995}, whereas
there is some chemistry in \citet{Thomas2008}.

Some parenthetical citations: \citep{Graham1995}
and then \citep[p.~56]{Thomas2008}.

\citep[See][pp.~45--48]{Graham1995}

Together \citep{Graham1995,Thomas2008}

\bibliographystyle{plainnat}
\bibliography{learnlatex}
\end{document}

You can see that we can cite different entries in the database by giving their key. The natbib package offers both textual and parenthetical citation styles, \citet and \citep, respectively. The reference style is selected by the \bibliographystyle line; here we’ve used the plainnat style. The bibliography is actually inserted by the \bibliography line, which also picks the database(s) to use; this is a comma-separated list of names.

Page references can be added to the citation with an optional argument. If two optional arguments are given, the first goes in front of the citation label for a short note and the second after the label for a page reference.

The setup above uses author-year style, but we can make use of numeric citations. That is done by adding the numbers option to the natbib line.

The biblatex workflow

The biblatex package works slightly differently to natbib, as we select the databases in the preamble but print it in the document body. There are some new commands for this.

\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage[style=authoryear]{biblatex}
\addbibresource{learnlatex.bib} % file of reference info

\begin{document}
The mathematics showcase is from \autocite{Graham1995}.

Some more complex citations: \parencite{Graham1995} or
\textcite{Thomas2008} or possibly \citetitle{Graham1995}.

\autocite[56]{Thomas2008}

\autocite[See][45-48]{Graham1995}

Together \autocite{Thomas2008,Graham1995}

\printbibliography
\end{document}

Notice that \addbibresource requires the full database filename, whereas we omitted the .bib for \bibliography with natbib. Also notice that biblatex uses rather longer names for its citation commands, but these are all quite easy to guess.

Again, short text before and after the citation can be inserted with the optional arguments. Note that the page numbers need not be prefixed with p.~ or pp.~ here, biblatex can automatically add the appropriate prefix.

In biblatex, the reference style is picked when we load the package. Here, we’ve used authoryear, but there is a numeric style and many others are also available.

Choosing between the BibTeX workflow and biblatex

Even though both the BibTeX workflow and biblatex get their input via BibTeX files and can produce structurally similar output in the document, they use completely different ways to produce this result. That means that there are some differences between the two approaches that may help you choose which one works best for you.

In the BibTeX workflow the bibliography style is ultimately decided by a .bst file which you select with the \bibliographystyle command. biblatex does not use .bst files and uses a different system. If you are using a template that comes with a .bst file or are given a .bst file for your project, you must use the BibTeX workflow and cannot use biblatex.

The different approach biblatex takes implies that you can modify the output of the bibliography and citation commands directly from your document preamble using LaTeX-based commands. Modifications of BibTeX .bst styles on the other hand usually require working with these external files and need knowledge of the BibTeX programming language. Generally speaking, biblatex is said to be easier to customise than the BibTeX workflow.

In biblatex it is generally easier to implement more elaborate citation styles with a wider array of different citation commands. It also offers more context-dependent features. Roughly speaking this is less interesting for the styles common in many STEM subjects, but becomes relevant for some more complex styles in some areas of the humanities.

BibTeX can only sort US-ASCII characters correctly and relies on workarounds to provide US-ASCII-based sorting for non-US-ASCII characters. With Biber biblatex offers full Unicode sorting capabilities. Thus biblatex is usually a better choice if you want to sort your bibliography in a non-ASCII/non-English order.

Having been around for much longer than biblatex, the BibTeX workflow is more established than biblatex, meaning that many publishers and journals expect bibliographies generated via the BibTeX workflow. Those publishers cannot or generally do not accept submissions using biblatex.

The bottom line is: Check the author/submission guidelines if you are submitting to a journal or publisher. If you are given a .bst file, you must use the BibTeX workflow. If you want a relatively simple bibliography and citation style and only need English US-ASCII-based sorting, the BibTeX workflow should suffice. If you need a more complex citation style, non-English sorting or want easier access to citation and bibliography style customisation features, you will want to look into using biblatex.

Exercises

Try out both the natbib and biblatex examples. For natbib, you’ll need to run LaTeX, BibTeX, LaTeX, LaTeX; for biblatex, it’s LaTeX, Biber, LaTeX. Find out how to do that in your editor, or try the Overleaf and LaTeX Online automation.

See what happens when you create new database entries and new citations. Add a citation that’s not in the database and see how it appears. Experiment with natbib’s numeric and biblatex’s style=numeric option.