Can Logseq synchronize to PDF annotations done in Zotero PDF reader?

I have now also tried to add highlights directly to the PDF using the application “PDF Expert” on my iPad (these annotations are stored inside the PDF). Unfortunately, Logseq cannot extract these, even though they are (obviously) shown in the Logseq PDF reader.
Note that Zotero does automatically extract these and shows them as “Extracted Annotations”. Something like that would be amazing in Logseq; e.g. automatically extracted annotations could be shown inside the page corresponding to that citation. It even seems preferable to using Zotero annotations, because you can add these annotations from any PDF editor and they are local to the PDF and hence easy to share.
Could something like this be implemented as a plugin?

Dear all,

I am new here and would like to start using Logseq, because its integration with Zotero. Logseq seems like an awesome tool for building knowledge from literature research and I am eager to jump in (kudos to the developers!).

After testing PDF integration with Zotero, I have found that annotations (i.e. text highlights) done in Zotero are not shown in Logseq and vice-versa. Through a bit of research, I have found that annotations in Zotero are not stored in the PDF, but in a separate database (see here). Same seems to be true for Logseq.

So my question is, whether Logseq is able to “pull” annotation from Zotero. This is important to me because I do most of my reading in the Zotero PDF reader, which works nicely on my iPad (also with Pen) and reliably syncs PDFs and annotations to my Desktop through WebDAV.

I have read other forum threads discussing PDF annotation export/integration from Zotero to Logseq (such as this one), but is not clear to me from that, what the status quo is and whether this is doable. I would also be happy with a (scriptable) work-around.

If this is currently not possible, is there something like this being worked on?

Thank you and best regards,

PS: These are my specs:
Logseq 0.8.7
Zotero 6.0.13
System: Ubuntu 22.04.1 LTS


Yes, I just tested this out expecting they synchronize both ways and realized the problem. Hope it is resolved soon, as I just setup zotfile addon for Zotero to work on the same pdf on the tablet too. My workflow would be much better

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Oh no… just when I thought I had found the perfect “PDF manager” with Zotero 6, with incredible editing and sync, turns out it’s not rrreally compatible with LogSeq. Which still has some maturing to do.

I’m newer to LogSeq than to Zotero. Does anyone know whether Obsidian, Roam, etc have better integration?

look here, and at this thread in general:

I did this for a while and couldn’t really abide it. I use now and prefer this workflow to zotero. Basically I read and highlight in Omnivore and do all the reference management in Logseq. The Omnivore plugin manages synchronization of the hightlights for me and each highlight can be linked back to the pdf. Your mileage will vary.

My take is this: staying 100% in logseq for everything including reading/annotating is the best. But this doesn’t work with, say, an iOS device as the reader/highlighter, because the pdf viewer only works on desktop. So if you can’t read with Logseq, then I think Omnivore has the best workflow right now. Ideally the logseq mobile client will gain the pdf reader functionality at some point but it seems like it is not currently on the roadmap, which is pretty irritating – because if we had iOS/Android pdf reading Logseq would be the magic solution to many problems that have not been solved anywhere.


I tried Omnivore for a bit. It looks very promising for webpages, but its PDF support is so bad it’s unusable. And PDFs are what interest me most. (In fact I think that even for webpages “printing to PDF” is the most reliable option)

Anyway, while looking into this I realised that a Logseq blog post from July 2022 says this:

I recommend also checking “Allow notes access” if you want to give Logseq access to your notes in Zotero. It can’t right now, but it should in the future.

So I think I will hang tight with Zotero and hope for improvements in Logseq. :crossed_fingers:

What’s bothering you in Omnivore’s pdf support? You might let them know.

I’ve moved over ~100 academic articles and full book pdfs to omnivore and read and annotated about 30 so far. I like the pdf workflow. I have had a few issues with getting a pdf to open in iOS from Logseq, but they have been isolated and (I think) related to spotty network connectivity… feels like omnivore doesn’t trap a network error in uploading properly… I reported that as a bug.

But I can finally manage resources in Logseq on my desktop, read and annotate on my ipad, and then get the annotations back into logseq with the benefit that they hold a hotlink that will take me to the doc and page if clicked. This is what I have wanted for quite some time.

Your mileage will vary, of course, but you might let the omnivore team know what’s up with the pdf support… they are pretty proactive it seems.

The Omnivore app I’m trying in macOS, v1.17, offers only scrolling the PDF. Doesn’t even allow highlighting. Even Apple’s stock readers are much more useful than that. It’s so basic that I won’t even try reporting anything.

I realize that the website (are they purposefully trying to be confusing?) has slightly better support for PDFs, but is still worse than Apple’s readers (needs more clicks for basic tasks, feels just like a beta or worse). And Apple’s is worse than Zotero’s (has no realtime sync, has no back navigation after page jumps).

The app that I am using allows paging vertical and horizontal or scrolling and supports highlights and notes. It appears to be better than other pdf annotation UX that I’ve used in the past and I’ve used most of them. I’m on v1.26.

Hi, (posting this again in all threads related to pdf annotations)

I was very frustrated by Logseq’s lack of pdf annotation import so I forked pdfannots to create a proof of concept to import pdf annotations. Here’s the link.

You can use it like so python ./ -f md_and_edn path_to_pdf -o path_to_pages_markdown --edn_output path_to_asset_edn.

This will create the markdown annotation file (in the pages folder) as well as the edn files containing the metadata of the highlights (in the assets folder).

This is still early and does not yet support highlight color parsing nor highlights different than simple text highlighting (no shapes, no rectangles etc). Don’t hesitate to help in the PR as I’m not a pro at this!


I was not able to make this work, but I filed an issue in your GitHub page for potential help.