I manage my research reference papers with Org-mode similar to [1].

Since I got an Android tablet I pretty much enjoy an automatism to
get the actual text of annotations and highlighting back to Org-mode
as well.

Take a look to [2] where I put an example shell script with
a short documentation.

  2. https://github.com/novoid/extract_pdf_annotations_to_orgmode
Karl Voit

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