After years of using Zotero, I recently moved all my bibliography (back) to BiBteX. In this article I briefly explain the rationale for this move. It might give some clues (of course, very personal and subjective) to other researchers who might be pondering  a similar decision. Another article gives some hints regarding the actual process of converting the database.

I like Zotero, and I think I know it pretty well by now. I've written/adapted a few export styles, two of which are now part of the Zotero Style Repository. I've written a plugin for Joomla to fetch, filter, sort and embed Zotero bibliographies in a website.  I've been advocating for Zotero and teaching its basics to a good many colleagues and students. However, over the years, I grew tired of some of its limitations.

What I don't like about Zotero
  • After years of using it, I (still) find its GUI cumbersome
    • It has too few keyboard shortcuts and they can't be customized.
    • I don't like how Zotero handles notes attached to publications. If I have for instance 15 notes for a book, I need to click/open each of them to get the full picture. Alternatively I could "Generate report from item", but then I can't edit the notes from that display.  
    • Its search system is slow and primitive, especially if one asks it to grep the full text (notes included).
  • I now do nearly all my writing in Emacs. This includes mails and academic texts. Having the bibliography in a different environment means unnecessary clicking and copy-pasting. 
  • I want the ability to link to a bibliography item from any text I write. Currently Zotero allows citing the item, but not linking to it (like: click on the link and it opens the item with its notes, attached files etc.).
  • in my emails I often need to cite some reference AND attach its PDF to the message. In Zotero, finding the PDF is a PITA.  
  • Synchronization with a server (for backup) or with a tablet (for reading) is possible, but:
    • I don't like being tied to for syncing my library
    • Zotfile is a great plugin that helped me a lot for handling the back-and-forth of reading and annotating stuff on my tablet, but it has some limitations of its own (in the way it automatically extracts annotations for instance). It also failed me a couple of times, deleting the ANNOTATED file from the synced folder before I could get it into Zotero (which meant basically that I lost all my annotations, since the deletion synced back to the server and then to the tablet).    
Where Emacs shines

Emacs solves all these problems

  • BiB(la)Tex has been there for years and it's well supported. There are wonderfully integrated tools to handle
  • When I need more, I can look into other tools like org-ref, or write my own. Extending Zotero is much more difficult, at least with my limited skills.
  • It's fairly easy to backup and synchronize both the .bib database and the .org notes using whatever tool one likes (including git, which brings in versioning and more). 
Advantages of Zotero

To be complete, I still see some strong advantages to Zotero 

  • Zotero makes it very easy to get a PDF into the bibliography. [OTOH that easiness also is suspicious. It turns out that Zotero sends the first pages of the pdf to some obscure server where there is a wonderful database that just recognizes most of those pdfs out there. It looks like only Zotero can use that database. What this means in terms of privacy is unclear to me.] 
  • Fewer people use Bib(la)Tex than those who use Zotero. In anthropology and ethnomusicology, I might be the only nerd using it nowadays. This could result in feelings of loneliness, cold, depression, and general inability to communicate with others. 
  • There are fewer citation styles already available. Customizing BiB(La)Tex styles might be a bit more complicated than working  with CSL. 

I had used BibLaTex in my PhD thesis. I later typeset that manuscript into a published book. BibLaTex proved to be manageable for me on both occasions. Having the bibliography and its notes integrated in the same working environment where I write my texts, talks and emails is very handy: same shortcuts, ability to link anything from anywhere, plain text formats easily tracked with git…  So after 10 years of using exclusively Zotero, I made the move back to BibLateX.  

In case anyone is interested, here are a couple elisp functions which I wrote to help me out in the conversion process.