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Currently I need to highlight certain sections in PDFs, or add annotations (comments/notes). These modifications would need to be saved.

What tools are out there to do this on Ubuntu?

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Have you looked at PDF edit from USC? – Mitch May 23 '12 at 16:54
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Have just tried pdfedit, ugly gui, no highlighting tools. It is not what i wanted. (if you are sure, give me instructions about how to do that with that pdfedit) – Anwar Shah May 23 '12 at 18:03
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I tried it, too. It has such tools in the toolbar above the text, but it didn't work as expected: When I tried to highlight text in a pdf I made with LibreOffice the area above the text became highlighted ... But than saving it the highlighting also is visible with Evince for example, although at the wrong place. → Not really a solution. – Jakob May 23 '12 at 18:09
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Google docs. I know it sounds like a cop-out at first, but it works and it will definitely be cross-platform. You can even download the result as a PDF containing the annotations you made – cxrodgers Jun 25 '13 at 10:07
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** UPDATE **: Native Foxit Reader now enables highlighting foxitsoftware.com/downloads – Orion Dec 7 '15 at 15:12

24 Answers 24

up vote 91 down vote accepted

Okular supports PDF annotations.

To save the highliting/annotations directly in the PDF document, choose "File" -> "Save as..." and create a new PDF which will contain your edits.

Edit: Inkscape supports PDF editing (one page at a time) and most people seem not to be aware of this so I'm adding it to the answer.

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Brilliant! Just what I was looking for! :) – ssanj Aug 7 '10 at 3:45
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Okular stores annotations and highlights outside of the edited document (it seems to be a Poppler limitation!) okular.kde.org/faq.php#addedannotationsinpdf This means that changes are only visible from Okular, on the machine they were created. – MarkovCh1 Aug 22 '11 at 23:10
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@downvoters: at least have the courtesy to specify why you're downvoting the answer. – Li Lo Oct 26 '11 at 13:59
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Inkscape allowed me to highlight text as well as 'redact' some personal information from a PDF by drawing opaque boxes over the text. Excellent solution, took ~30 seconds to install, about the same amount of time to edit my one page PDF. Thanks Li Lo! – OpensourceFool Jan 6 '13 at 22:48
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Okular can now save annotations to PDFs, see askubuntu.com/questions/1529/how-can-i-highlight-pdfs/… – Thomas Arildsen May 14 '13 at 9:29

Actually, none of these solutions work half as well as anything on Windows or Mac OS. Mendeley only supports yellow highlighting and importing pdfs into inkscape or openoffice is pretty inconvenient if you want to read a paper and simply make some annotations.

Fortunately, there are some free pdf viewers for Windows that work flawlessly with wine (If you find wine too complicated, use PlayOnLinux - a great front end for wine configuration). One of the best of those viewers is the PDF-XChange Viewer by Tracker Software. There is a free version that comes with a ton of annotation features, session saving etc. Grab it here:

http://www.tracker-software.com/product/downloads

And check out this screenshot:

http://www.tracker-software.com/image/Viewer1%28684%29_300x0.jpg

I really whish there was a working open source linux alternative (xournal is good, but too limited). But for the time being, I am happy with using wine.

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I'm sure Inkscape, pdfedit, or okular work at least half as well as some packages on MacOS or Windows. – belacqua Mar 20 '11 at 22:27
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+1: This is, so far, the only good option. It works great in Wine, mod some Unity-specific bugs that are getting fixed, and supports a wide collection of document markup options. – MarkovCh1 Aug 22 '11 at 23:08
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I normally use Foxit_PDF_Editor on Wine – blvdeer Jan 11 '13 at 18:44
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Okular can now store the annotations in the pdf itself – Hashken Nov 12 '13 at 23:16
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@Sadi: I have found the portable versions of PDF-XChange Viewer to work well with any WINE version I tested it (including 1.7.8 x64). So that's an option as well. And although your statement is true, it won't help if you have several modified but unsaved documents opened. – onse Dec 10 '13 at 21:26

xournal is also some software which you use for this task.

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xournal only saves the highlights in a xournal-specific format (basically converts the PDF to images, and highlights there) – MarkovCh1 Aug 22 '11 at 22:10
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@Szygy :In contrast to okular xournal can however export the annotations to PDF – Glutanimate Sep 16 '12 at 9:42
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I just used Xournal for annotating a PDF file, and exported the annotated version to PDF, and it worked perfectly. – Erel Segal-Halevi Mar 20 '13 at 10:28
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@ErelSegalHalevi Please disregard my last comment. Recent revisions of Xournal do not rasterize the PDF. Both text and scalable vector elements are preserved. This make Xournal the best choice for PDF annotation by far. – Glutanimate Apr 21 '13 at 19:22
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One of the nicest little features in xournal is that you can use pressure-sensitive pen input, and even these scribbled annotations will be saved as vector graphics, not images. Means, small file size all around. – tanius Oct 28 '15 at 11:36

Future version of Evince will support PDF annotation and highlight. Here you can see a video of the first partial implementation, made by Carlos Garcia Campos

If you want to try I think you need to have at least evince 2.32 and recompile yourself latest version of Poppler cloning from the git repository:

git clone git://git.freedesktop.org/git/poppler/poppler

Here the launchpad bug of this missing feature from evince (poppler packaged for Maverick isn't enough updated).

21 april 2011 - Update Evince in Natty now support by default annotations (not highlighting). Evince in Natty is 2.32, poppler is 0.16.4.

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I have 12.04, evince 3.4.0, poppler 0.18.4, and I can't find the annotation feature in the menus... – Erel Segal-Halevi Mar 20 '13 at 9:29
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It can be do in the side pane now. (I have not tried with 12.04.) help.gnome.org/users/evince/stable/annotations.html.en – Arpad Horvath Jul 29 '14 at 6:26
    
It's not really highlighting but more adding notes to the documents – shaneonabike Sep 20 '14 at 20:43
    
Indeed, in 14.04 you can also access Annotations in the side-pane, and add comments/notes. You can then save a copy, and it shall be compatible with Adobe Reader. A bitten hidden from the user, but nifty stuff. – landroni Jan 24 '15 at 18:36

There is a package called pdfedit that can do this.

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Note that pdfedit has been dropped from Ubuntu as of 12.10 – Dustin Kirkland Dec 17 '12 at 22:22
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Also, on 12.04 there are some errors, such as, when trying to change the color or font. Also, pdfedit has no undo, which can be very frustrating, especially since the highlighing does not work as expected (highlights a full line instead of a single word). – Erel Segal-Halevi Mar 20 '13 at 9:27

The PDF viewer in Mendeley allows you to highlight and annotate PDFs. To save the modifications you need to File > Export PDF with Annotations.

However Mendeley is not open-source, and it forces you to use an account... But otherwise the functionality is excellent.

You can download from here.

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While Mendelay has a nice interface, the annotation abilities are limited (can only add sticky notes; no drawing or text boxes), and annotations and highlighting aren't saved in the document. – MarkovCh1 Aug 22 '11 at 23:06
    
@MarkovCh1 In my experience they are, if you Export PDF with annotations. – landroni Jan 24 '15 at 18:38
    
What I love about Mendeley is its ability to export a page in the end of the PDF, listing all the annotations. Pretty cool. I hate though that it's not open-source, and that it forces you to use an account... – landroni Jan 24 '15 at 23:42
    
Mendeley does not currently support adding/deleting bookmarks – titus Nov 14 '15 at 16:15

Recently a new version of Foxit Reader is released for Linux. It has the highlighting and annotating support. It has more annotation options than Okular, including inline notes with transparent background, drawing of various shapes etc.

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Great! It is fast, lots of options, saves everything to a single file, thus suitable for annotation. After downloading, make sure the .run file is executable. Also, you might wanted to edit mime types ~/.local/share/applications/mimeapps.list after installation. – VRR Oct 24 '15 at 15:42
    
can you add more steps how to install this? I can't find it after installation. – buzhidao Jan 13 at 2:16
    
Please check this answer. It provides the necessary steps to install the software. askubuntu.com/a/679213/421047 – Gobinath Jan 13 at 4:38
    
if foxit released a new version, than this is easily the best answer, foxit is the best pdf viewer on windows, been looking for an alternative for it on linux, good to know they updated it – Lynob Jan 24 at 21:20
    
This should be upvoted more. The new version works quite well, with much more annotation options than Okular. – JI Xiang May 1 at 5:26

There's a plugin for OpenOffice.org that does this.

http://extensions.services.openoffice.org/project/pdfimport

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Now you can actually export annotations to PDFs in Okular (this was not possible until recently): http://docs.kde.org/stable/en/kdegraphics/okular/annotations.html

It seems Okular has to be built with Poppler at least version 0.20. It works with Ubuntu 13.04.

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For me the best solution was PDF X-Change Viewer.

It just installs and works flawlessly under Wine. (Source)

The only issue is that sometimes when you scroll fast it shows some white spaces over the text, that clear when you click or select a line in the document.

There is an option in the Edit menu under Preferences\Performance\Threads Usage: "Use synchronous mode of page rendering" which prevents those white spaces in mine.

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Yes, PDF X-Change with Wine is the best solution, but that is what user11305 had already replied. – mivk Jun 1 '15 at 9:52

The evince package which is built-in in Ubuntu and is called Document Viewer can add annotations to PDFs. Starting with Ubuntu 15.04, Document Viewer can also remove annotations. The version of evince to be released in Ubuntu 15.10, version 3.16.1, does not support highlighting, however...

Evince 3.18.2 from the the Ubuntu 16.04 default repositories has support for adding highlight annotations, as well as squiggly highlight annotations and moving text annotations.

If you do not have a visible side pane on the left side of the opened document's window, click View -> Side Pane or press F9 to make the side pane visible. At the top of this side pane, there is a dropdown menu with options like Thumbnails, Index and Annotations (some of which may be dimmed for some documents).

To create an annotation:

  1. Select Annotations from the dropdown menu. You should now see List and Add tabs under the dropdown menu.

    enter image description here

  2. Select the Add tab.

  3. Click on the icon to add a text annotation.

    enter image description here

  4. Click on the spot in the document window you would like to add the annotation to, preferably a blank spot where the annotation will not cover anything else in the document. Your annotation window will open.

  5. Type your text into the annotation window. You can resize the note by clicking and holding the left mouse button on one of the bottom corners of the note, and moving it around.

  6. Close the note by clicking on the x in the top corner of the note. You might need to hover over the x with the mouse to make it visible.

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I was searching for exactly the same. For me, qpdfview works like a charm, is simple to use and lightweight. Its annotations and text highlighting is recognised in Adobe Reader (Linux version 9, Windows. iOS). Editing done on the aforementioned platforms are recognised by qpdfview as well. It allows you to delete annotations and highlighting too, and stores annotations in the PDF.

It is free, the source code can be found on launchpad. You find it in the Ubuntu Software Center and there is a ppa for a more recent version: ppa:b-eltzner/qpdfview

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In qpdfview 0.4.16, annotations can be created using CTRL+a. Then, one creates a rectangle and chooses "Add text" or "Add highlight". This is very different from Acrobat Professional 8.1, where I can select text and then choose whether I want to add a comment, delete the text, add text or replace the text. – koppor May 8 at 14:06
    
Yes, true. The reader is using Poppler which has the "Investigate better (that is, normal) text selection" as a ToDo now for a long time: cgit.freedesktop.org/poppler/poppler/tree/TODO – Marcus May 9 at 12:49

Jarnal is a good software that allows you to highlight

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I have got a workaround to this problem, but it is too localized. Using okular for reading a pdf file and then annotate by pressing F6 to bring Highlighting toolbar.

After annotating, you can save the file as document archive, which preserve the annotation. From File -> Export as -> Document Archive.

Note This file can only be opened by Okular.

Installing Okular: To install okular, issue this command in terminal :
sudo apt-get install okular

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You can just do Save As now in Ubuntu 13.04 :) – shaneonabike Sep 20 '14 at 20:44

I've tested PDF X-Change viewer and I experienced the same white space problem while scrolling. I'm currently using Foxit Reader 4.3 which works really flawlessly. Foxit 5 crashes with wine 1.3 but works fine with wine 1.4 and 1.5. The only minor bug is that when you add a text annotation, it will ask you if you want to download the dictionary. You simple click cancel and keep working. It will keep asking you just once every time you open Foxit.

I managed to make Foxit reader 4 my default pdf viewer but can open files by double clicking a pdf file only if Foxit is not open. With Foxit 5 this issue is solved too. See this thread: How do I set a wine program (ex. Foxit Reader for Windows) as the default program?

Hope the pdf annotation feature in evince improves to avoid using wine.

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I use an old version of Foxit Reader (the latest 4.x version from oldapps.com), and it works very well under Wine.

At the moment, there is no good native highlighting solution!

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Master PDF Editor is a good software for annotating PDFs. There is a free version for non-commercial use.

Features:

  1. Adding images to PDF
  2. Adding/editing bookmarks
  3. Opening PDFs in tabs
  4. Adding sticky notes to PDFs
  5. Adding Ellipse, Rectangle, Lines
  6. Highlighting, striking out, underlining texts

I think it works just like Foxit reader for windows. Advantages over okular:

  1. In Master PDF Editor you can save PDF in a normal way without the need to saving PDF using "save as".
  2. In okular as far as I know you can't add or edit bookmarks but in Master PDF Editor you can easily do that.
  3. In okular you can't add images to pdf, But in Master PDF Editor you can.

Disadvantage over okular:
It uses too much RAM.

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+1 but if others are interested in this, the commenting functions are much less powerful than, say, Foxit or PDF-XChange Viewer. It's very powerful in other ways (e.g. editing the pdf itself), but not as saving comments per se. You can add shapes and text directly to the pdf, but these won't save as the comment layer. Changing the format of the highlights, etc. is also very fiddly (need to open up setting every time). – Sparhawk Apr 18 at 12:48

I think that Xournal is the tool you're looking for. What you should do is exporting in PDF, and the changes will be saved in pdf.

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Maybe xournal (app to add annotations to pdf's files)

Click to install xournal

And okular save the hightlighting separetly then if you want to save the hightlighting you have to save the pdf like new file to save the hightlighting.

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I have tried saving as new file. Did you try that ? – Anwar Shah May 23 '12 at 17:31
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This saves the highlighting to be part of the PDF in a way that can't be edited in other PDF editors, if I am correct. – MarkovCh1 May 23 '12 at 17:31
    
I really like Xournal but when you export Xournal annotations as PDF it saves an image of every page with the annotation. So when you send that pdf to someone else, they will not be able to search through it. Other than this main limitation, Xournal is pretty cool. – Aras Aug 5 '12 at 7:55
    
I just used Xournal, and the file were saved as a searchable PDF. Excellent. – Erel Segal-Halevi Mar 20 '13 at 10:29

PDF Studio is, probably, the best solution. It is not free, but you can install it using the Ubuntu Software Center.

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I had the same question but unfortunately I didn't arrive to any satisfactory answer, being okular the closest one (but as you say, it does not save the changes in the same file, which is a problem).

I finally decided to use "PDF-Xchange Viewer": that piece of program makes exactly what I wanted to do and does it well, but it has two problems: it is free but not opensource and there's no linux version, although it can be used in ubuntu via wine. I wish there were better ways to annotate PDFs and so on.

Maybe you could open an issue at okular developers so hopefully they can implement that feature in the nearly future.

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You should also try PDF Buddy, an online PDF editor that supports highlighting, annotation, and other common editing features. It's a fast and easy solution that works in any modern browser.

(Full disclosure: I'm a co-founder of PDF Buddy)

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The latest version of Ubuntu's default PDF viewer Evince has a built-in highlighter. It is very efficient. And unlike other softwares, the highlighted text is also detected when we open it using other softwares like Adobe PDF Viewer. The version number is 3.17.4 and you can download it using the link below:

https://github.com/GNOME/evince/releases

Please note that you have to first remove the old version of Evince before you install the new one. Also, the program crashed few times on my first day of install but it is totally fine for a month now.

~Cheers~

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I got good results when annotating and editing PDFs online using PDFescape. There's a limitation on file size (10MB) and number of pages (100) though.

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