About the annotations in PDF file in logseq

Actually, this feature request is a little bit complicated.
I am currently using Logseq to read references and get involved in scientific researches. I am comfortable with the PDF annotations linked to the PDF file. When I click it, I can get the locations of the annotations in the PDF file. However, I have some questions when I have two different computers with different operating system. Specifically speaking, Windows and MacOS.

  1. I am a PhD student and I read references everyday. So Zotero integration in Logseq is what I want to appreciate most. It is really fantastic since it can help you to organize the reference pages. However, in two different operating system, the Zotero attachments file locations are different. For example:
    Windows: C:\Users\John Doe\Zotero
    MacOS: /Users/John Doe/Zotero
    This seems natural since we are discussing two different systems. However, this will cause a problem when you annotate one PDF file in Windows system and want to backlink these annotations to where they are in MacOS system. I wish the developers can attach importance to this question because it will really benefit us a lot.
  2. I am actually confusing about the Zotero Profiles in Logseq. What is its function? I actually tried to set up two different Zotero Profiles in two different operating systems in order to see whether the annotations will still backlink to their original PDF files or not. But I failed. I will appreciate it very much if the developers can consider this problem.

Hi, (posting this yet again to 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 ./pdfannots.py -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!

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@XiaoFeng_Li Logseq currently does not support relative paths, see

There are some workaround, such as hardlinks from your assets folder.

There are also different ways to support Zotero, natively (using the Zotero Web API), or using plugins (GitHub - sawhney17/logseq-citation-manager)

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I made a functionnal script that can be found here: Python script to import pdf annotation to logseq