Note Taking and Annotating PDF Documents

Using Jarnal

Installation Instructions | Jarnal Wikipedia page

1. Install Java if you haven't already
2. Download Jarnal from http://www.getdeb.net/app.php?name=Jarnal
3. sudo dpkg -i jarnal*.deb jarnal
4. Run jarnal
5. Click on Format ... Paper and Background ... and select Plain instead of lined paper
6. Click on File ... Open Background and open your pdf file
7. Annotate the text using any of the many tools provided by jarnal
8. Click on File ... Export ... Export to PDF
9. Enter the new file name and click on Print PDF

If you ever have a problem where opening the output file in a pdf viewer results in the annotations being shifted, it means that the original pdf document had some strange invisible header. Open the original file as a background and export it to pdf without doing any annotations. Then open that pdf file as a new background and proceed.

Using okular

If you are using KDE 4 (e.g., with Kubuntu 9 Intrepid) you can use the built-in okular document viewer to annotate pdf files using the review mode. Annotations are saved in an xml file inside ~/.kde/share/apps/okular/docdata so only other okular users can view them, and you will need to give them the appropriate xml file to install in the aforementioned directory. You can't have okular save the pdf file after annotating because this will not save the annotations.