Giving up on PDF annotations

What I wanted: To be able to seamlessly take notes on PDFs with the annotations automatically synced to my notes. Additionally, if I make any changes to any of the annotations at any time, they must also immediately sync back to my notes. 

Is this possible?: Note that this workflow for HTML is possible using WebResearcherJS ( along with Joplin. 

However, after exploring this issue for a considerable period of time, today, I give up on my pursuit to integrate PDF annotations directly with my research workflow. I am prepared to label this task as 'possible but time-consuming and challenging to implement'.

Solution adopted: Instead, the solution I adapted was to iframe the pdf on to a webpage and use WebResearcherJS to take notes on the webpage. Thus far, this pipeline works like a charm and eliminates the need to directly deal with PDFs.


  • Python: I wrote a python module that extracts PDF annotations. One possibility is to run it every time a pdf in a folder changes and sync it with a note taking app.
  • Among the note taking tools I explored, LogSeq has the best PDF annotation integration. It also stores the annotations as markdown files, so in theory one could use this as a starting point.This is close to what I had in mind but there is currently no straightforward to export the annotations along with the pdf. This is problematic. 
  • Taking notes on a good (by this I mean functional) presentation program (e.g., LibreOffice on LInux) might also be a good avenue to explore as well.



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