Scientific Workflows with Zotero

It’s quite frustrating, I must say, to see that the open source community is now, in 2022, finally able to start replicating the functionalities of a (relatively simple) commercial tool that had figured all of this workflow out about 10 years ago: Citavi. PDF highlights, annotation with page numbers that can be (1) tagged (2) categorized in multiple hierarchical trees, a plug-in that connects to word and shows this hierarchy in the text editor, automatic formatting of references…It’s all been there perfectly working and integrated (without the need to export, re-format, etc). Except of course it’s closed-source, becoming expensive, built on an outdated Microsoft database structure and is basically unable to move out of there (the web app is a joke).

If only Zotero and Logseq developpers could take a good hard look at Citavi and say: we can do that and much better, we would gain a huge amount of time. Anyway, in the meantime, we re-invent the wheel with the tools we have…For the time being, Citavi is such an efficient workflow that I’m willing to install a virtual machine and run Windows 11 just to be able to use that program. But I can’t wait until the day that I can switch to a good Zotero/Logseq integration…


I agree 100% - Logseq was my choice after trying most of the PKM apps around. However, I became incredibly disappointed to learn that there is no way to make notes on PDFs and then create a document where the references are automatically added (ie. parent block PDF citation).

Citavi is the model here. One can take notes, comments, quotes on PDFs and add them to Knowledge sections or chapters. And then in one click generate a Word document of these, with bibliography generated.

I highly recommend that Logseq put some resources toward solving this, via a plugin if needed. Even in the “Move Block” plugin, a left click for “Copy with ref” and then pasting giving the block with the reference as [[@reference_name]] would work find since we all probably prefer Latex anyway.

Will this be possible?


Could you describe this in detail? Does it directly relate to PDF, Zotero, Citavi, “Move Block” plugin etc. or is it a functionality on its own?

I was just describing a fast way to implement this, perhaps through the “Move Block” plugin. The main point is to have comments under a PDF link back to the PDF when inserted into a new note (presumably an outline of your paper).

See here for more thorough ideas: PDF Annotation: Copy Text With Block Ref, Citekey, and Page Number

Generally, we need to 1) Insert a PDF in any block, likely from Zotero and have a citekey 2) have any comments/blocks under that PDF include the citekey when added to a new note. Thus, using the Zettlekasten method we could quickly write new articles by opening a new TOC and adding relevant notes, and they would be “automatically” cited.

To be clear, this is just the fastest way and it could be built up a bit over time, by having preferences in citation type, format, etc.