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 Except of course it’s closed-source, becoming expensive, built on an outdated Microsoft database structure and is basically unable to move out of there (the web app is a joke).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.
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).
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.
Hey,
I’m working in academia and have been using LogSeq for ~1 year now. I really like it and much prefer it to all the other stuff out there. I think in theory the workflow with Zotero is ideal. You can gather your literature, annotate specific passages and easily find what you read a year ago without having to reread 10 papers.
However, several issues are becoming more and more of a bother for me.
When importing papers from Zotero, the search takes about 15 -30 seconds (which is just a lot more than it needs to be).
The Logseq pdf viewer is still quite buggy and really doesn’t compete with native viewers. (I still use it because I like the annotation feature, but I feel like it’s slowing me down a lot) I reported a bug report here
For some reason the authors are not rendered correctly so that I end up with something like this:
authors:: (“Alexei Baevski”, “Arun Babu”, “Wei-Ning Hsu”, “Michael Auli”) even though all of the authors are in double brackets.
I looked into the zotero better notes Plugin and I think it does look quite nice, I just don’t know if maintaining the zotero notes being synced with Logseq is going to get annoying after a while. Also for some reason none of the links in the Markdown files that I export from Zotero work. But that seems to be an issues for multiple people here. I’m just unsure if it’s more feasable to have all the pdfs annotated directly in Zotero indipendent of Logseq or if having it all come together in Logseq makes more sense. I guess there are arguments for both, but the idea behind Logseq very much is gathering it all in one place to be able to interconnect your notes. I’d be happy to hear what other peoples thoughts are in that regard. Anyway, sorry for that brain dump, hopefully someone found something useful in it somewhere.
I’m excited to see what the database update in Logseq will bring in terms of latency. The community here makes me optimistic that it’s worthwhile sticking around.
I haven’t found a good solution either. I’d tend more towards annotating documents in Logseq, but the viewer in Zotero is a bit more stable and convenient.
Zotero search is really not great, even Zotero+Word is barely usable. The best solution I’ve seen is to search the Zotero db with an external program:
It’s sad that fzf can search a text file with a database dump an order of magnitude faster than Zotero can search itself, IMO they made some bad design decisions.
fzf can call external programs, the external program could then call the Logseq API to insert the reference at the cursor.