I also discovered the zotero-roam-export plugin a few weeks back and opened an issue about the markdown export. It didn’t look very promising, so I’ve since then spent some time writing a plugin for Zotero that works for my own workflow.
I only briefly used Zettlr, and so far I don’t see myself using Obsidian to write papers directly, so I don’t need the full citation powers that Zettlr offers (at least so far!). In my case, even pandoc has its limitations, which is why I end up writing the paper using LaTeX anyways. For me, Obsidian is useful to keep my (often private) notes, and relating ideas from what I’ve read or highlighted to some other idea that I’m working on, which is why I keep two different files for the same paper: one with my notes linking to the one with the information for Zotero (that way, if needed, I can fully rewrite the latter with a (newer) export, without losing my notes in the former).
The plugin I wrote is based on the zotero-roam-export plugin and in short, my plugin does the following:
- Extracts metadata from the item and highlights from the PDF using Zotfile (similar to
zotero-roam-export) and saves it in a markdown file. I get one file for each item selected. I can save directly in my vault, and I can (optionally) choose to use cite keys (using Better Bibtex) as file names e.g.doe2020aaaa-zotero.md - Creates a file for my own notes based on the naming above (minus the suffix)
doe2020aaaa.md, and transcludes the metadata, links to the highlights/annotations, and adds a header for my notes. This is the one I use to link when I refer to the whole paper and as a sort of table of contents around specific ideas of that paper, i.e. I can “cite” the paper as[[doe2020aaaa]]. - Adds all those files as linked attachments to the Zotero item, so that if I double click the markdown note is opened with the default markdown app from Zotero (if eventually the URL protocol is implemented, then the link can easily be switched to include
obsidian://). This basically lets me go from one app to the other. In Obsidian, in thedoe2020aaaafile I can write my own notes, and in preview mode I can also click on a link in that opens Zotero and selects the right item. In Zotero I can double click to edit my notes, or open it in Obsidian.
If this sounds like it might be useful to someone here, I can share the Zotero extension.
Disclaimer: This is my first time coding anything Javascript or Zotero-related and I can’t really guarantee that it will work well or efficiently. I learned a lot and reused some parts of the zotero-roam-export in order to get the plugin working for myself (so far so good).
Finally, I have a question for those that use Zettlr or want a Zettlr-like way to cite within Obsidian. What does your (expected) workflow look like? Do you use Zettlr/Obsidian to create PDFs and render citations? How would the citation in Obsidian look like? Do/Would you also create a note for the paper itself? And if so, when do you “cite” and when do you link to the note, i.e. [See @doe2020aaaa] vs See [[doe2020aaaa]] ?
Edit: Here’s the plugin https://github.com/argenos/zotero-mdnotes
The standalone post with my workflow (slightly updated since) is here: Zotero plugin to export metadata and notes to markdown