The Living Thing / Notebooks :

Citation management

How a 21st century researcher proves their ideas are important enough to present through 20th century infrastructure in the manner of a 19th century gentleman

The genealogy of truth is important and there are many important ideas about how we could track it, especially with advances in technology; However, this page is not about that propagation of evidence that the practice of citation was developed to support, but rather the pragmatics of the charade of of evidential support that actually-existing academic publishing requires.

In particular, how can I get my journal-ready citations in the 1890 format required by my journals with the bare minimum of dicking around? Moving citation workflows forward into the 1940s can be accomplished by someone else with time.

Citation traumas to avoid repeating

For my own part, I use Zotero. This option is open source, powerful and hackable. It could be more user-friendly; but then the competitors set the bar so low that this is hardly a criticism. Slightly more user-friendly but less hackable is Mendeley, a closed-source reference manager that also is not awful.

Since I have no patience for things that cannot be automated, Zotero is an easy choice for me; You may wish to try both.

There are other options such as Papers (meh) and Sente (ugh!) and (sigh) Endnote. I won’t link or refer to those further here, for the reason that I’ve already lost too much data that way, and I don’t intend to lose more. I can’t in good conscience advise anyone else to waste their precious time.

Still, if you’re keen: For any closed-source software my advice is the same — Try and see how well you can get data in and out, en masse, because that’s what you’ll have to do if the company goes bankrupt or gets bought by Google and shut down, or by Yahoo and accidentally set on fire, or by Facebook and you are only allowed to use it if you click on ads promoting sports shoes for 18 minutes out of every hour.

All the alternatives apart from Mendeley and Zotero have failed the test of preserving my precious data when I exported it to a different software package, so using those other packages is putting my work in the uncaring hands of an unaccountable third party. To actually extract my data from Sente I had to burn a whole working week turning their malformed markup into valid XML, (which is a specialty that I don’t care about and no-one should ever need to care about) and I still couldn’t work out how to parse some of it. Then many other things went wrong.

If you mostly care about LaTeX (which decision is constrained by the lowest common denominator amongst your collaborators) you might be able to survive on Bibdesk or jabref or just editing a plain Biblatex file, but I for one could not bear to give up the browser integration of Zotero, which has saved innumerable hours of painstaking pointless typing.

See also text editors, academic writing workflow.

TODO: complain about the entire structure of citations in the electronic age (keep it short though, because everyone is tired of complaining about it, and at least it’s better than the general howling void of unsourced internet media.)

TODO: apologise for accidentally complaining at length despite my stated aim of keeping it short.

Zotero

My weapon of choice.

The main lesson from my outdated previous citation management page:

Zotero has an API with which you can both read and write data. So do Connotea and Bibdesk. But Zotero’s API is cleanest, and has an active community around it, and I don’t feel that I am locking my data away forever if I rely upon it. (Of course, you can always try to migrate data around from anything to anything with BibTeX, but if you have URLs in there, or consort with foreigners who dare to have diacritics in their names, this usually leads to trouble). I can use the API to make changes that I couldn’t make manually, without worrying about that parsing nonsense. Since all citation software is, basically, awful, it is even more important that whichever application you choose, it is one that you can get your data out of it when you find a less awful option. Moreover, some other apps, such as Mendeley, already use the Zotero API, so you know that it’s not going to be a community of one playing with it[…] Also, Mendeley started behaving suspiciously since they got bought by Elsevier

Useful hacks

Better BibTex

a.k.a BBT.

Here are some citation key format strings for bibtex.

[auth:fold:nopunct][Title:fold:nopunct:skipwords:select,1,1][year]

I currently use this one

​[auth][veryshorttitle1_1][year]

I am fond of the following biblatex export exclusions:

file,abstract,note

Zotero for your tablet/e-reader

to be evaluated, the currently active clients seem to be

or you you use zotfile to synchronise a folder full of attachments to your tablet. That’s what I do. It’s not perfect, but it’s easy and robust.

Plaintext citing for your website/blog

tl;dr. There are many over-engineered solutions. The style file one is the simplest I’ve found, and it should additionally work for anything which supports CSL. This includes Mendeley at the least, and possibly Papers. Others?

Anyway, if you want a more fragile but fancier solution, there are other options below.

Render using a CSL style file.

Screencap of Zotero

Slightly weird, but robust and simple.

It’s ugly, because it has to battle with a grumpy rich-text XML infrastructure to render plain text, but it gets the job done without any coding, and is robust against software changes.

pandoc and markdown

See also markdown.

The preferred pandoc-citeproc format seems to be something with an @ sign and/or occasional square brackets

Blah blah [see @heyns_foo_2014, pp. 33-35; also @heyns_bar_2015, ch. 1].
But @heyns_baz_2016 says different things again.

This is how you output it.

# Using the CSL transform
pandoc -F pandoc-citeproc --csl="APA" --bibliography=bibliography.bib \
  -o document.pdf document.md
# or using biblatex and the traditionalist workflow.
pandoc --biblatex --bibliography=bibliography.bib \
  -o document.tex document.md

You will need to set up Preferences>export>Default format to be Better Bibtex citation key quick copy and set Better Bibtex to copy pandoc style.

See the pandoc manual and the pandoc-citeproc manual.

See also the markdown/pandoc page for more on this.

docutils-based

a.k.a. Citations in ReST.

I no longer recommend this. For all the laudable design goals and extensibility of ReST, it’s not where the community is. They are all using markdown.

But if you are keen, the docs say:

Standard ReST citations are supported, with the additional feature that they are “global”, i.e. all citations can be referenced from all files.

I can add:

For your comfort and convenience these citations will be rendered as born-obsolete fugly 1995-esque hard-coded HTML tables that no-one in the entire internet has managed to whip into anything other than an eyesore in a decade of vain struggle.

More resources.

Web-native solutions

For general blogs there are a few suggestions below.

For jupyter etc I filed the suggestions under scientific workbooks.

These can avoid the need to create bibfiles, rendering bibliographies directly rather than going through bibtex, which is a good thing for websites.

zotero citation

For Atom+Zotero+Markdown, you could try zotero citation. References look like

[\(Heyns, 2014\)](#@heyns2014)
[\(Heyns, 2014\)]([email protected],heyns2015)

The bibliography is rendered in either pandoc-YAML or plaintext format at

[#bibliography]: #

I don’t bother; BetterBibtex works fine for my needs.

They are rendered in the output by an in-built pandoc filter, which is installed separately:

Misc

Oh, BibTeX

None of that faffing about is useful if you are working with academics, who don’t regard words on the internet as a real thing. Your words must be behind a paywall where no-one can read them to count as significant. Moreover, they must have been rendered harder to analyse by running them through LaTeX, and obfuscating them into a PDF, which probably also entails using BibTeX to do the citation stuff.

If you are starting from Zotero, you can use Better BibTeX to make this less painful.

To manage annoying BibTeX problems from BibTeX files themselves algorithmically I use bibtool.

Biblatex/biber

Mild upgrade from the winding labrynth of character set errors that is bibtex. You often need to use bib styles made by passionate bibligraphy rendering fans, e.g. here is an IEEE-like one.

To mention

Jabref, bibdesk, biblatex vs bibtex vs biber, character set sadness.