Use Biblatex/Biber to create a new subdatabase based on an auxiliary file

October 5, 2016

(NB: I discovered this feature of Biblatex/Biber by searching for a way to replicate the very same feature in JabRef, which I no longer use.)

Sorry for the title gore. Here is what I mean. Suppose you’re writing a paper called paper.tex that uses a BibTeX database (bib file) called master.bib containing all of your references. Normally, of course, paper.tex doesn’t cite every single entry in master.bib, but only a subset of them. Suppose now that your paper has been accepted in some journal, and you need to submit your bib file to the typesetters. Obviously, you don’t really want to submit your entire master.bib, but you also don’t want to manually extract the subset of entries actually cited in your paper. Well, it turns out you don’t have to: you can automatically create a new bib file containing exactly that subset by using biber (the backend processor to Biblatex). Here’s how. (NB: In paper.tex, you have to use the biblatex package with biber as the backend processor. This won’t work with regular bibtex. Use bibexport instead.)

Step 1. Run pdflatex paper.tex, which will generate the auxiliary file paper.bcf.

Step 2. Run biber --output-format=bibtex paper.bcf.

(You can leave off the .tex and .bcf extension in both commands.)

This will generate a file paper_biber.bib containing all entries in master.bib that are cited in paper.tex. At this point in our made-up scenario, you would probably rename paper_biber.bib to something like refs.bib, change the \addbibresource line in paper.tex to use refs.bib, recompile everything to make sure it all works, and finally submit paper.tex and refs.bib to the journal.

One quick follow-up note. By default, biber will put entry names like @article and entry fields like author in all caps:

  AUTHOR = {Mary Smith},

I personally like having everything in all lower case, because I don’t like my bib entries to yell at me (of course, as far as biber is concerned, it doesn’t actually matter: it’s all cosmetics). You can tell biber what to do by using the --output_fieldcase flag. The possible options are upper (default), lower (my preference), or title (e.g. InProceedings).

There are a bunch of other output options, too. For example, you can specify the output filename (e.g. --output-file=refs.bib), whether to align entry fields in neat columns (--output-align), how many spaces to indent entry fields (e.g. --output-indent=4), and so on. See biber --help, in particular everything starting with --output-*. Here’s an example command.

$ biber --output-format=bibtex --output_fieldcase=lower --output-file=refs.bib paper.bcf