unfolding disasters/ posts/ BibTeX

BibTex is system (tools and file format) for managing references in LaTeX documents. Forget about formatting your bibliography (is it “publisher (year)” or “publisher: year”?), just add entries for the works you're referencing, and drop in a \cite{key}. I also use my entrez script to pull nicely detailed citations off PubMed and its related databases. Once you've added the citation to your database the first citation, you can reuse that data in any future paper just by reusing your BibTeX database. It's wonderful.

Basic usage

At some point in your LaTeX document:

\bibliographystyle{prsty} % Phys. Rev. style

other syles include abbrv, alpha, plain, unsrt, ... In your LaTeX document where you want the bibliography:

\bibliography{wtk} % wtk.bib is the name of the database

compile (using latex for example) with:

$ latex example
$ bibtex example
$ latex example
$ latex example

Formatting names

There are many possible author name formats, but the least ambiguous is von Last, Jr., First Middle. If the von is capitalized (e.g. "Emanuela Di Cola"), use \uppercase:

@String{EDCola = "{\uppercase{d}}i Cola, Emanuela"}

See Tame the BeaST for details.

Natbib

I don't actually use LaTeX's \cite{key} command as I claimed above. That works, but the Natbib package adds support for other citation styles & link formats. I actually use \citep{key} (parenthetical citations), \citet{key} (textual citations), and other more specialized Natbib commands. That way I don't have to worry about misspelling author names or remembering “et al.” when I cite a source in the text.

Makebst

Customize bibliography with Makebst (latex makebst, from custom-bib), makes .bst (bib-style) format files according to your specifications.

Cross-references (more like sub-references)

Don't repeat yourself! BibTeX lets you piggyback low level references (@inbook, @inproceedings) underneath higher level references (@book, @proceedings) without duplicationg information from the parent entry (via crossref). However, this can be a bit tricky.

Like a number of TeX tools, BibTeX tries to accomplish as much as possible with a single pass through your data. This makes things more memory efficient (if you really can't spare that extra MB ;), but it also makes for some odd errors. While working on my thesis, I ran into:

$ bibtex root
…
Database file #9: root.bib
Warning--string name "nist:esh" is undefined
--line 1175 of file root.bib
A bad cross reference---entry "NIST:gumbel"
…

The problem is due to the @inbook entries occuring after the @book they reference:

@book{ NIST:ESH,
  …
}

@inbook{ NIST:gumbel,
  crossref = {NIST:ESH},
  …
}

When it's reading your bibliography, BibTeX hits the @book entry (NIST:ESH), and says to itself, “Hmm, it doesn't look like anyone's referencing NIST:ESH. I'll save some memory by forgetting I've seen it.” Then when BibTeX hits the @inbook entry (NIST:gumbel), it says, “Ahh, this references NIST:ESH. I'd better keep an eye out for that.” Unfortunately, this is too late, because it's already past that entry. BibTeX hits the end of the database without finding a (second) NIST:ESH definition, and complains about the missing reference.

The solution is just to order your @inbooks (and other crossref consumers) so they occur before the entry they reference:

@inbook{ NIST:gumbel,
  crossref = {NIST:ESH},
  …
}

@book{ NIST:ESH,
  …
}

Embarassingly, this information is spelled out on Wikipedia's BibTeX page:

The referred entry must stand below the referring one.

That's the kind of thing you'll only remember after you've been bitten by it ;). Hopefully putting the bad cross reference error message in the surrounding text will help the rest of you searching for solutions.

It looks like Matěj Cepl (who has also contributed to rss2email) ran into the same issue back in 2000. It's a small world ;).

References

There are a number of good resources to get you going: