Re: Citation processing via Zotero + zotxt

[John Kitchin <jkitchin@andrew.cmu.edu>]

I clearly had some super important academic work to do today, so instead
I played around with citations ;)

I am not yet convinced a citation processor will get us where we want
because of the complexity of the external dependencies, and the
potential/probable need for us to define new CSL files for different
backends, or at a minimum for org-formatted citations and
bibliographies. Hacking bst files is no fun, and it doesn't look like
CSL files are much better! Plus you have to find them and install them
somehow.

I wanted to get a sense for how well I could manipulate citation and
bibliography format from org-ref with a bibtex database. The answer is
it is pretty easy, not perfect, but pretty good, and could certainly be
made better with dedicated effort. You can see how here, and some
discussion about its limitations:

http://kitchingroup.cheme.cmu.edu/blog/2015/12/03/Exporting-numbered-citations-in-html-with-unsorted-numbered-bibliography/

I am pointing this out because I think the approach I used could allow
for plugins for different database backends, different ways to get the
replacements, etc... you could substitute org-ref links for the citation
syntax at some point with no real loss of generality. org-ref could
insert the new syntax as soon as it is available in a main org branch.
Some code will have to be rewritten to get the key under point, but that
probably won't be too hard.

We could provide a solution like this for some backends, using bibtex as
the database, for pretty immediate use. Then other more advanced
solutions could come along that would likely be superior in output
quality if they use real citation processors, but only if there are CSLs
for different backends (if I understand how they work). These would be
optional, and only needed if higher quality and flexibility in output
was required.

What do you think?




Matt Lundin writes:

> Richard Lawrence <richard.lawrence@berkeley.edu> writes:
>
>> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>>
>>> 2. How would I use this starting from an org-bibtex database (which I
>>>    typically export to bibtex)?
>>
>> I can envision a couple of possibilities.  One simple option would be to
>> switch to managing your reference database with Zotero, by exporting
>> from org-bibtex to .bib, and then importing the .bib into Zotero.
>>
>> I don't want to force that on anyone, though.  Another option is to
>> use the org-bibtex to produce .bib at export time, and then use Zotero
>> to read the .bib and process citations when exporting to non-LaTeX formats.
>>
>> This second option is more work, as I don't know of any API for loading
>> items into Zotero's citation processor in BibTeX format.  But given that
>> Zotero is able to import .bib files, I imagine this API would not be too
>> much work to build.
>
> Given these complexities, it seems that if we went the zotero route we
> could end up with a fairly large installation chain (firefox, zotero,
> zotxt, plugin for zotero). And this would require installing items from
> multiple, heterogeneous sources.
>
> I wonder at this point whether pandoc-citeproc (packaged with pandoc)
> would actually be the simpler route. It can parse bibtex files directly
> and (as a filter within pandoc) can output formatted citations in org
> format.
>
> As a GNU/Linux user, I would find installing zotero and all the add-ons
> messier and more cumbersome than installing pandoc and/or node-js (were
> we to use citeproc-js) from the command line.
>
> Best,
> Matt
>
> Footnotes:

--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu