Bibliography Management

2023-01-17
last updated 2023-06-07

I recently received a request to outline my process for managing bibliographies. Here's a breakdown of my approach.

I use the Zotero application as a reference manager. The Zotero Firefox connector ¹ lets me add papers from URLs. Zotero is quite smart about grabbing the metadata from the URL or PDF itself.

The view I have from Zotero is:

While Zotero is great for storing local copies of papers and generating bibliographies, I don't find it to be optimal for organisation and note-taking. Instead, I use the Zotero Better Bibtex plugin to export all the items in my library² into a BibLaTeX file that I reference items in with another application.

I'm using Obsidian as a front-end into my Git repository of notes as plaintext markdown files. I have Zotero exporting its bibliography into this directory as references.bib, tracked with version control, which I then interface with using the Obsidian Citations plugin. This allows searching the bibliography in Obsidian, referencing items in the bibliography in Obsidian notes, and creating notes for bibliography items in Obsidian. I find this to be much more flexible than Zotero's in-built note-taking functionality: notes can be version controlled, can link to each other, and can other notes can reference bibliography items.

To organise references for a project, a note associated with the said project can reference all relevant papers. And speaking of organisation, the plugin Obsidian Kaban provides a convenient way to maintain a reading list.

The graph view from Obsidian, with bibliography items notes in red, is:

This approach is quite modular. Zotero could be replaced with another reference manager that can generate a BibLaTeX file, or be omitted entirely and the file manually maintained. Obsidian could also be replaced with another note-taking application that can interface with a BibLaTeX file, or indeed one that doesn't if the user doesn't mind manually maintaining reference keys.

However, with slightly tighter integration we can get some benefits. Using the following Obsidian Citation plugin template:

title: {{title}}
authors: {{authorString}}
year: {{year}}
citekey: {{citekey}}
DOI: {{DOI}}
zoteroSelectURI: [{{zoteroSelectURI}}]({{zoteroSelectURI}})
URL: {{URL}}

---

We have not only a link to the URL (if it exists), but a clickable link to the local Zotero entry and the associated PDF with zoteroSelectURI.

There are still a few outstanding issues with this approach, though:

There is no way to generate a bibliography with only the items referenced in a project note, e.g. for creating a bibliography.bib for a paper.
There is no support for PDF annotations of papers. I'm currently using the reMarkable 2 to read and annotate papers, which is great while on the go and for saving paper. Currently, I'm using rmfakecloud to sync PDFs to the device and back up annotations. Some integration of annotated PDFs in this workflow could be useful.
There isn't a clear path to collaboration. One possibility would be sharing a Zotero library out-of-band ³ and then separately collaborating on a shared Obsidian note repository. However, the Zotero library could become out of sync with the contents of the repository's bibliography file. Instead, perhaps managing separate bibliographies would be appropriate, and just committing sensible changes to the bibliography file references.bib in the note repository. Another problem is that having a separate Obsidian note repository wouldn't allow linking to notes created here in a personal note repository. To remedy this, using a git subtree of this shared repository in the user's personal note repository might make sense.

Please get in touch if you have any suggestions for improvement.

Bibliography Generation

Note-taking

Conclusion