Marking comments and annotations on top of a PDF

Question

I occasionally receive PDFs on which I want to mark comments, or some points/segments of which I want to annotate somehow - similarly to what I would do with printed PDFs.

This does not mean editing the contents - which stays just as it is - only addition of (clearly differentiable) comments - "red pen" style - on the page.

So - I want a piece of software which does this.

Required features:

• Works on Linux
• GUI of course
• Does not mess up the layout of the PDF (i.e. additions-only)
• Reasonable responsiveness on "heavy" and long PDF documents

Note I haven't listed a license requirements

Desired features:

• Gratis
• Libre license
• Can save the PDF-cum-comments as another PDF file, which will display properly, with the comments, in a typical PDF reader
• Actively maintained
• Offers extra functionality when noticing the PDF was created a certain way, e.g. with LaTeX, or LibreOffice, or Microsoft Office etc.
• Supports both comments and annotations
• Supports multiple comment authors (e.g. with different color comments)
• Doesn't make it easy to edit the PDF when I don't want to edit it.
• Allows extracting/saving the comments/annotations as plain text or some other format convertible to plain text.

Answer 1

So far I have been using Xournal for this purpose and I am quite happy with it. It essentially allows you to draw on top of the PDF using text and primitive drawing routines.

Regarding your criteria:

• Linux – yes
• GUI – yes
• additions-only – yes
• responsiveness – I haven’t had any challenging cases yet, but so far everything works fine.
• gratis – yes
• Libre license – yes, GPL
• Can save the PDF-cum-comments as another PDF file – yes, with some people using exotic software had problems with my PDFs, but those could be fixed by using a PDF printer instead of the native PDF exporting function.
• Actively maintained – yes, last update was two months ago
• Offers extra functionality when noticing the PDF was created a certain way – no
• Supports both comments and annotations – not really. You draw on the PDF, so the comments do not make use of a special PDF functionality intended for this purpose.
• Supports multiple comment authors (e.g. with different color comments) – Makeshift. You can comment with multiple colours, but there is no explicit collaborative functionality or similar that I am aware of.
• Doesn't make it easy to edit the PDF when I don't want to edit it. – Yes, editing the PDF’s text is impossible.
• Allows extracting/saving the comments/annotations as plain text or some other format convertible to plain text. – Not that I am aware of.

Answer 2

I would suggest taking a look at Elsevier's Mendeley research paper sharing and management software, and its desktop client specifically. Note that it is a lot more than just a PDF annotation tool it is a research tool that covers a lot more areas.

It allows you to annotate PDF files with:

• General Notes i.e. notes on the whole file
• Sticky Notes i.e. notes with specific locations
• Text Highlights in multiple colours
• Area Highlights in multiple colours

All annotations are tagged with who added them & when.

Required features:

• Works on Linux desktop client: Yes & Windows & Mac OS There is also a web interface and iOS/Android apps.
• GUI of course Yes
• Does not mess up the layout of the PDF (i.e. additions-only) Yes
• Reasonable responsiveness on "heavy" and long PDF documents I have not had any problems

Desired features:

• Gratis Yes for the Free Account with some limitations currently 2GB personal document storage, up to 5 private groups of up to 25 people with up to 2GB of storage across all groups. Additional storage via paid plans
• Libre license No this is a commercial tool aimed specifically at academia
• Can save the PDF-cum-comments as another PDF file, which will display properly, with the comments, in a typical PDF reader Yes "Export to PDF" does this giving you a choice of exporting the annotated document or just the annotations
• Actively maintained Yes
• Offers extra functionality when noticing the PDF was created a certain way, e.g. with LaTeX, or LibreOffice, or Microsoft Office etc.
• Supports both comments and annotations Yes
• Supports multiple comment authors (e.g. with different color comments) Yes You can select colours and all comments & highlights are marked with who & when.
• Doesn't make it easy to edit the PDF when I don't want to edit it. Yes The comments and highlights are stored separately from the PDF the original file does not get changed at all.
• Allows extracting/saving the comments/annotations as plain text or some other format convertible to plain text. Yes You can use the tool to export to several academic formats (BibTex, Research Information Systems & Endnote XML) - there is also a GPL python tool Menotexport available for exporting to text files which is both command line & GUI based last update to Menotexport at the time of writing was 8 days ago.

Answer 3

Okular supported annotations for some time, but since recently, you can also save the annotated PDF using the native PDF annotation format. You can mark specific text passages and add a comment to this; you can also place comments not anchored to a specific text and draw freehand or straight lines, polygons, and ellipses. I recently used this for annotating proofs of a paper and reports I graded and it could do everything I wanted.

Regarding your criteria:

• Linux – yes
• GUI – yes
• additions-only – yes
• responsiveness – I only tested short documents so far.
• gratis – yes
• Libre license – yes, GPL
• Can save the PDF-cum-comments as another PDF file – yes, since version 0.15, requiring Poppler 0.20 (according to several sources)
• Actively maintained – yes
• Offers extra functionality when noticing the PDF was created a certain way – no
• Supports both comments and annotations – yes
• Supports multiple comment authors (e.g. with different color comments) – Each comment shows its author. Different colours are not supported.
• Doesn't make it easy to edit the PDF when I don't want to edit it. – Yes, modifying the underlying PDF is impossible.
• Allows extracting/saving the comments/annotations as plain text or some other format convertible to plain text. – Yes, Okular stores annotations in an XML format in your config files (.local/share/okular/docdata/ for me).