Annotating pdf documents in Papers

Until recently, when asked whether Papers provide good annotation tools I would say “not really… but they have other advantages …”. There is no longer need for such an excuse. Papers’ support for document annotation is as good as in their competitor, Sente. This feature is so elegant that it’s almost easy to miss.

  • select a piece of text, right-click and choose either Highlight or Make a Note:
  • if you choose to highlight, the highlighted text will be transferred to the Annotation;
  • if you choose to make a note, whatever you type will also appear in the Annotation.

By right-clicking on a highlighted piece of text you can change the highlight color or perform other functions, for example copy all annotations from the document to the Clipboard.

About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He researchers energy and environment and coordinates MESPOM, a Masters course operated by six Universities.
This entry was posted in Annotation, Bibliographies, Files and tagged . Bookmark the permalink.

22 Responses to Annotating pdf documents in Papers

  1. René says:

    Sadly you can not make a comment on a highlighted section. And in case you add a note it is up to Papers to decide whether or not this comment shows up before or after the cited/highlighted parts of text. Finally, I found the selection of text way less reliable compared to other programs. Therefore I continue to use PDF Expert on the iPad for now. Still looking for a good PDF highlighting/annotation tool for the Mac, tough.


  2. jp says:

    Unfortunately that’s not true (as good as their competitor). Four main reasons:
    1. Once highlighted, the annotation text from the pdf is not editable. This makes it useless for annotating ocr’ed documents where minor corrections are needed, or for inputing notes into the body of the quote itself, shortening it, etc…
    2. Papers still does not have image annotation / clipping tools like sente. Graphs, diagrams and photos in documents cannot easily be annotated or put in the notes panel. This is especially useful for long documents.
    3. Whilst neither program is capable of correctly judging the correct order of highlights (especially when there is more than one highlight per page) and page numbers, sente at least allows you to change the order or page number of the annotation. This is very important so that when you print the resume of annotations, they are all in the right order.
    4. (somewhat unrelated) (i) Unfortunately, when searching for authors or titles of documents, the papers search window is buggy – it does not always return all the documents in the library, even after double checking the search terms. This is what ultimately made me give up on papers, along with… (ii) hard to customise bibliography styles.
    Points 3 and 4(i) are what ultimately made me give up on papers, even though it is so much more fairly priced than sente.


  3. Qadir says:

    Unfortunately, there is no way to make free-hand highlighting or hand-written notes with stylus either in Mac or iPad versions. I use PDFpen on iPad and Adobe Acrobat on Mac for this, but it is hard to combine them with Papers. Unfortunately, Apple dislikes stylus input–or may be they just could not figure how to make it usable…


  4. René says:

    I’m curious. Does anyone of you know a Mac app that allows the annotation of highlighted parts in PDFs and their export into a text file (just the way PDF expert or Goodreader for iOs do)? The only software I found with this feature is the horrible Skim. There has to be something better. PDFpen/pro doesn’t have that functionality, neither has the built in Preview – nor any other software I tried.


    • Aleh Cherp says:

      Many thanks everyone for their comments. Perhaps Papers should indeed further improve its annotation capability. However, the way I deal with annotations (i.e. transferring them to my notes and eventually to my writing) the ability to copy highlighted text and notes (Copy Annotations) to the Clipboard is pretty sufficient. When reading an article I usually don’t want to get distracted with writing an elegant review at the same time. Thus I do not really care whether my highlighting is accurate, spelling perfect etc. I just want to make very quick messy notes. If they go further I will edit.


      • René says:

        Thanks for the reply. I read your great blog for quite a while now, but this is the first time I finally find the time to add a comment.

        I also copy/paste the highlighted sections and the comments in a text file; then I split up this file into many smaller pieces (one idea=one .txt file) and add OpenMeta tags to each of them (via nvAlt). Later on I use DevonThink+Ammonite or Leap to find these pieces. For this workflow it is crucial that the highlighted text comes before the right comment. Sometimes Papers manages to do this correctly, sometimes it doesn’t.

        And that is why I love PDF Expert on the iPad so much – it is by far the best solution to highlight text in a PDF, add a comment to the highlighted section and then export both into a text file/email. I haven’t found something equally good for the Mac yet.


    • Ez says:

      Curious why Skim doesn’t work for you? It’s not as pretty as others but it does its job – some interesting applescripts around (export notes OPML, export by highlight colour etc). I’d love a pdf program that allows hotkeying highlight colours though (or some sort of applescript). I have to agree though that papers2 doesn’t work for me for annotation – but then neither does Sente. When I’m marking up I want to do it in the least possible steps…even that extra click to choose highlight every time I need to highlight a passage becomes old very fast. Hotkeys + Bettertouchtool + Magic touchpad = seamless annotation.


      • René says:

        Only fairly recently I made my peace with Skim and now use it along with Papers. It took me a while to figure out how to edit the text in highlighted sections and how to add a comment to it. For me these are the most important things of the annotation process. I rarely highlight a passage without having the urge to add a few words as a comment to it. In Skim you have to double click on the highlighted section and then you will be able to add a comment or to correct the OCR where necessary! Maybe it is only me but it took quite a while to figure that out.

        ps. How do you use Bettertouchtool?


      • Ez says:

        I actually hate trying to annotate without an external multi-buttoned mouse or my magic touchpad now. Bettertouch tool lets me set gestures per program, so for Skim I use left and right tip-tap to select my two most frequent annotation tools (highlight and underline), three finger tap to select the arrow line (which i use to draw my attention quickly to main points).
        I use two finger tip-tap for anchored notes (I usually put one at the very top of the paper to add random notes or a brief summary of the paper) and to undo (if I highlight the wrong thing etc…a peeve about Skim is that you can’t just keep enlarging a highlight like in preview for when you miss a word or two).
        Because annotating is mainly a mouse related activity (in terms of highlighting, markup…not adding notes) I find it easier and much quicker to bypass the keyboard when I can – so having the hotkeys work as gestures (or mouse buttons- which is what I used to use) just makes the process seamless for how I work – I don’t have to move my hand over or think about pressing key combos so it’s a fraction of a second in switching between the different tools. It may not seem a lot but it does add up.


      • René says:

        Interesting. I guess workflows are just a very personal thing. I always need/want to add some notes to interesting passages. Yet, I also don’t link moving my hands – but they usually rest firmly on the keyboard.


      • René says:

        Btw how do you handle Skim and Dropbox? It seems really difficult to get those annotations synced.


      • rapsoe says:

        Ez: in Skim you can add words to an highlighted section by merging notes using the Shift key. Not the best way to implement such a feature, also there’s no way to do the reverse, but this may solve your problem.

        On another note, selecting text in Skim with the “option” key pressed helps avoid a lot of spurious characters in OCRed PDFs.


  5. Elle says:

    That’s a fair point Aleh, even when I am using Writepdf on the ipad once I am finished it can look messy! But then for me that app does what it is supposed to do and it’s been ideal for proofing on the go and solved me a lot of bother!


  6. amafortas says:


    I agree with many of points about how useful Papers can be. However, I’ve noticed that the note icon used to indicate an annotation will sometimes obscure text in .pdf documents. Have you found a way to work around this? (I can’t seem to get the icon to move.)




  7. John Minard says:

    ‘Just discovered this excellent discussion!

    ‘Seems incredulous that there isn’t a simple way to do referenced notes on selections in a PDF. A simple workflow for me (as others have suggested) would be: highlight text in a PDF; add a small note associated with that text; export all annotations for the PDF in a format that lists sequentially: Document title, page number, each highlighted text followed by its note.

    Perhaps a programmer could tell us why this is difficult. Understandably text in the PDF format may not be easily addressable in a linear way (eg. in multi-column docs, and where graphics interrupts the text, etc.), but I would settle for being able to do this on the Mac in any standard text-only format – epub, RTF, Pages, Word, even ASCII.

    ‘Anyone know of a way to accomplish the above workflow on a Mac, in any way, shape, or form?

    Thanks Aleh, et al.
    – John


    • Ez says:

      Hi John,
      Unfortunately there just isn’t a dream program out to do this with minimal fuss. Papers2, Sente and Mendeley all offer the possibility of annotations in the form of highlight/notes. However, none of these really do it for me. My solution is to keep my references in Sente or Papers2 and do the annotations in Skim. My experience so far has been as follows:

      Paper2 offers highlighting by holding down the cmd key and it automatically copies the text as a quote over into the note pane, you can change the colour via rightclicking on the highlighted text. You can’t add your own notes to that quote though in the notes pane or change any of the text in case it copies over wrong. You also can’t change the page numbers it sets and I haven’t had a great deal of luck with it recording the right page number (you can hide only one cover-page – occasionally I get two) and for some odd reason even if I have say a page 12-24 journal article, I hide the front page and it indicates the first page as 11 , un-hide it and the highlight on the first official page of the journal becomes 13… odd. You can add your own notes to an anchored icon, however they started disappearing for me before I could write anything. If you don’t want to anchor notes so that they appear at a specific point though you can write them in the notes pane or in a popup. I was using Papers2 fairly seriously as my main reference manager since I love the “manuscript” function. However I begin to find citations weren’t coming together correctly and having no proper way (apart from copying a citation and viewing it in the clipboard) of previewing the formatted citation got to be a huge bother.

      Mendeley I haven’t spent much time with as I find it has less to offer me than the other two. While you can highlight and add notes here too, highlight seems to be only highlight rather than quote. Notes appear on the paper as the usual icon and pop as a sticky note, then appear on the notes pane, however you can’t change the page number.

      Sente offers highlighting, quoting and commenting features in a popup that appears when you highlight text on a pdf. Highlighting does just that while quoting and commenting will highlight the text and put the same colour sticky note in the notes pane. If you chose quote then the text is copied over also. The sticky note has a place for a title, a quote, and a comment and also has a page number. Again, you won’t always get accurate page numbers but the definite advantage is that you can manually change the page number… it’s just depending on the amount of notes it can be annoying. My quirk with annotating in Sente was that highlighting and then clicking got somewhat annoying when I just needed to highlight. There was no way to keep the highlight tool always on. It’s only a little thing but it annoyed me enough to seek an alternate method. You can export notes in all programs mentioned here I think, it may require the use of applesript though (you can easily find them by a google or in the programs forums – i used to use a sente script to export the notes as OPML for easy import into devonthink or Scrivener).
      In terms of pdf management I’ve recently moved back to Sente because I find that preview window with the formatted citation essential and it seems to format them properly. If you want to stick to annotating in a reference manager then this would be my go to for the simple fact you can change the page number if you need to, the 3 sections in the sticky notes are handy, and it hasn’t malfunctioned on me so far 😛

      Now for annotation, I personally use Skim; It’s an open source pdf reader. All annotation features are hotkeyed for ease of use which speeds up productivity whether you’re keyboarding or program the hotkeys to the magic trackpad like I do. Whenever you highlight (or underline), the text gets automatically copied over into the annotation pane. You have to double click on the actual highlighted passage to open the notes box where the quote is – then you can change the text or do what I do… put a space and then AN: followed by whatever notes I have. Alternatively you can add an anchored text note which will appear in the notes pane in sequential order with the quotes so that as you’re looking over it later it’s all in the order of whatever is first on the page. Arrows and lines etc also create a place in the annotation pane in the same sequential order and you can add a note to go along with them if you like. I admit I like the use of arrows to draw me to particularly important passages as I tend to over-highlight. You can also add notes that appear on page in little text boxes and again the notes contents will appear in the annotation pane. From this point you can export the notes which will turn everything into RTF (or whatever format you chose) … once in RTF format you can manually change the page numbers if you wish.
      It’s not without its own downsides though. It’d be nice to be able to drag a highlight if you need to extend it. As is you need to delete the thing and start again. You can’t see Skim annotations in other programs unless you export the paper as a pdf with embedded notes. That can be a dealbreaker; it’d be nice if the highlights and marks on the pdf show up like they would in a preview document. A personal quirk I hate too is that you can’t highlight text with the text select tool and then highlight it. You have to pick the highlight tool and re-highlight. It’s a minimal annoyance though.

      I haven’t found a single other PDF reader for mac that copies over the highlight for quoting other than Adobe Acrobat X (I think previous versions did too but it’s been a while since I used those…). It didn’t format quotes neatly though (breaking up the text into random new lines). Again it offers page numbers but you can’t edit them in program so it’s going to start from page 1 like skim. I found it ugly (uglier than Skim which is pretty sad) and clunky too – not all of the annotation tools were hotkeyed which is a problem for me. Also changing highlight colour wasn’t as simple as it needs to be. I’d still kill for a program that allows hotkeying different colours!

      There are a number of applescripts around for skim – e.g. export note depending on highlight colour (potentially handy since Skim doesn’t write what highlight colour something is in the annotation pane so there is no distinguishing them if you export your notes and would have liked to distinguish them this way) . Also there seems to be one by the same guy to get Skim to recognise actual page numbers of a pdf… I haven’t looked much into it though – it’s a little beyond me and I don’t have the time currently to figure it out at the moment. They can be found here: (check the sidebar for the other Skim related posts).

      Whew… I hope any of that was of use to you! If you find a better way then please do let us know 🙂



      • This is a great introduction to all the issues in doing annotations on the Mac and also summarizes my experience. If not reading on my iPad (using PDF Expert), I use the Skim/Papers combination described above. I also would kill for iOS quality PDF reading on the Mac.


  8. Pingback: Guest post by Ez: Annotating PDFs in Papers, Sente, Skim and other apps | Academic workflows on Mac

  9. Precisely how long did it acquire u to publish “Annotating
    pdf documents in Papers | Academic workflows on Mac”?
    It possesses quite a bit of superior details.
    Thanks ,Amparo


Leave a Reply to Wan Park (@wpark) Cancel reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s