Thank you for the well-done right up! I can’t say that am a power-user in Zotero yet so perhaps others can fill in their experiences, but here are my thoughts on some of your questions:
How to split workflow between Zotero and Logseq
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Has anyone done an in-depth comparison between Zotero and Logseq PDF annotation? Are there any downsides of Logseq?
- Zotero 6 Annotation Pros:
- Text Search
- Can edit highlight annotations
- Highlight annotations have appropriate spacing between lines (there is an extra space between words at the end of a line and the first word in the next line which is missing from logseq highlight annotations).
- Can highlight images
- Can export annotations to Zotero’s new note format (at the cost of cloud space if you have image annotations), and then export to markdown (I have not tested how it works with image annotations)
- Very stable (no data loss or links breaking)
- MarkdownDBConnect plugin in Zotero can link to Obsidian, logseq and other software to add an icon on articles in the Zotero Database. This helps differentiate between articles I have created a note for in Logseq and others that I haven’t made a note for yet. It’s simple to setup especially if you’re using citekeys as your markdown file names.
- If I annotate the pdf file directly, the annotations show up in the sidebar similar to if I made the highlight in Zotero. However, I can’t edit the highlighted text.
- Zotero 6 Cons:
- As you mentioned, there is no note or article linking feature which logesq is best for.
- Without exporting annotations are stuck inside Zotero. However there are hyperlinks at the end of each annotation that can open local Zotero when we need to see the context.
- Logseq PDF Annotation Pros:
- Highlights text and images that can be easily referenced anywhere in logseq.
- Highlight annotations can be edited to include anything that can be rendered in logseq (mathjax, code, bold, italics, links…)
- Zotero settings in logseq allows for importing of links to pdfs from our Zotero database.
- Logseq PDF Annotation Cons:
- No pdf text search
- Image Highlights don’t work with Zotero PDFs with spaces in the name: github issue. There is a small fix for that currently in the issue comments, but requires file renaming with Zotfile.
- Current Zotero plugin in logseq isn’t customizable like the one in Obsidian (no customizable template for yaml properties) which results in creating too many pages for all the authors. The search option is also very slow compared to Obsidian and shows less information (missing the authors, year of publication). Otherwise it does what it needs to do.
- UI zoom scaling resets while editing or resizing the logseq window. When that happens the view also resets to the beginning of the file.
- If the pdf file has highlights already, they do show up in the logseq pdf viewer, but they don’t fill up the logesq annotation file, unlike in zotero.
The most stable and consistent workflow I would think is to take all my notes on Zotero, and then export the notes and images to markdown. Unfortunately I’m more used to taking notes and summarizing as I read which leads to me annotating in logseq more. The caveat here being I need to screenshot figures and diagrams instead of linking in image annotation since that is still buggy at the moment.
If the logseq team fixes zoom scaling bug, and image highlight bug with zotero pdfs, then I think the workflow where zotero is used to capture articles and logesq for annotation and linking would work well. Especially for those who work mostly with text and less with figures/ diagrams.
Note: I use Windows 10