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PDF's can be annotated with comments and highlights. I believe the data of such annotations are typically stored in the meta data of the PDF file itself. However, there is also a separate format for saving the annotations next to the PDF (https://www.adobe.com/devnet/acrobat/fdftoolkit.html).

The OS application Skim implements something similar and allows you to save annotations as a .skim file (https://skim-app.sourceforge.io/manual/SkimHelp_43.html).

Mendeley also seems to implement separate annotations, as opening the PDF files with a different viewer will not show the annotations (https://www.mendeley.com/guides/desktop/04-read-highlight-annotate). However, it is unclear to me where these annotations live.

Foxit Reader allows the user to import and export annotations as a separate .fdf file, but it requires multiple additional steps and clicks by the user (https://www.foxitsoftware.com/blog/using-comments-data-import-and-export/).

Having a separate annotation file can be helpful for multiple reasons, including working with a Git repository where the PDF's are uploaded once (or even gitignored), while the smaller annotations file is tracked by Git.

Is there software for Windows which allows you to annotate PDF documents and which can by default save these in a separate file and by default load the annotations when opening the PDF?

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    Mendeley stores annotations separately on their servers and possibly usefully splits annotations for a given file on the view that you are using so that you can have private annotations & shared. – Steve Barnes Mar 10 '18 at 7:38
  • Also an automatic comment extraction tool would do the job, since the world uses Acrobat to annotate pdfs – Julian_W Mar 11 '18 at 10:04
  • @Julian_W Yeah, potentially. Though key to my request is the automatic part, both in extracting the annotations for saving and sharing, as well as automatic in loading the annotations when opening the pdf file. – LBogaardt Mar 11 '18 at 15:48
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On Linux I use Xournal for this, which saves annotations etc. into an external file in XML format – and can be configured to automatically open that file along with the main PDF. Xournal is also available for Windows from the linked page.

Xournal
Xournal screenshot (click to enlarge)

The XML format used by Xournal has another advantage: You can always edit that directly to fix some markers, be it text corrections or aligning the positions.

I'm using Xournal for over a year on Linux, and I'm quite satisfied. Only doing "light stuff" with it, though – and of course it takes a little "getting used to".

From their manual: "A journal is composed of one or more pages. Each page consists of a background and one or more layers stacked on top of the background. All drawing operations take place within a single layer. Xournal can be used to annotate PDF files, by loading the pages of a PDF file as backgrounds for a journal. By default, the PDF file used to generate the backgrounds will not be saved with the journal; instead, the journal file will contain a reference to the absolute location of this file."

  • Awesome! This will do. Not exactly the PDF annotations I was hoping for (so if anyone else has suggestions, please answer), but certainly a useful tool. – LBogaardt Mar 10 '18 at 12:54

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