I’ve seen a few people here use Zotero. I ended up writing a plugin to export metadata and annotations much like the
zotero-roam-export plugin. It’s sort of made for my own workflow, but I thought I’d leave it here in case someone finds it useful: https://github.com/argenos/zotero-mdnotes
What I use the plugin for:
- Extract metadata from the item and export the highlights from the PDFs using Zotfile (similar to
zotero-roam-export) and save them in markdown files.
I get one file for each item selected.Originally I was using a single file per reference, but I’ve found it better to have more atomic notes, and I extract highlights based on color as described here. The metadata file contains links to the highlights/annotations. All those files are saved to a folder in my vault, and I can (optionally) choose to use cite keys (using Better Bibtex) as file names e.g.
- Create a file for my own notes based on the naming above (minus the suffix)
doe2020aaaa.md, and transcludes the metadata 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
- Add 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 the
doe2020aaaafile 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.