Guest post by Ez: Annotating PDFs in Papers, Sente, Skim and other apps

Ez responded to the post on annotating pdf in Papers with a comment so useful I reworked it, with Ez’ kind permission, in a separate post. It was prompted by John asking about a “simple workflow”:

‘… [to create] referenced notes on selections in a PDF […]: 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 … I would settle for being able to do this on the Mac in any standard text-only format – epub, RTF, Pages, Word, even ASCII.

Here is Ez’ response with some technical edits:

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 :P

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 :)



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, Writing and tagged , , , . Bookmark the permalink.

6 Responses to Guest post by Ez: Annotating PDFs in Papers, Sente, Skim and other apps

  1. Vincent says:

    Concerning cover pages and Papers2, the solution I use in order to get correct page numbers for text highlights is as follows:
    1. Import pdf to Papers2, match to correct metadata etc.
    2. Right-click on pdf icon, open with Preview.
    3. Delete cover page(s), save file.
    4. Papers2 will now ‘see’ the correct page numbers.


  2. Hi Aleh,
    Great post!

    I’ve been using skim and taskpaper for annotations. I used papers2 but after reading your post, I was excited with the possibility to edit notes right on skim!
    I’m exporting edited notes from skim and importing into taskpaper. The main problem with skim is that when used with papers2 you have to export the file to the correct folder to sync the annotations. And it doesn’t have an iOS app too.
    But for annotating, skim is the king. While reading it allows me to “tag” some highlighted paragraphs. I use the “@…” syntax at the end of the text and then I export this to Taskpaper.
    When imported into taskpaper this “@…” becomes contexts and you can search and work only with the tagged paragraphs for writing. I use the reference, papers link and magic citation as the the “project” title and all notes are indent to this title. When I select the context (@methods, i.e.) I can see all different articles with that tag and can easily cite them during writing (I usually copy the magic citation).

    As it is plain text, Taskpaper files can be imported (or indexed) into devonthink and even edited there (or anywhere else)! It also has a great iOS app that can sync through dropbox.
    I used to work with omnioutliner for writing and outlining, but now I prefer taskpaper for that as it has some outline possibilities, some great applescripts and syncs with dropbox and iOS. Designed primarily as a simple task management app it can be used for the project related planning too and it is much easier then omnioutliner to manage projects.
    The same dev released a great app recently, called Folding text, that has some similarities with taskpaper, but is even better for writing. It is still quite new and lacks (but will support) tags/contexts and some other features. But it is much better for outlining!
    I’ve done a screencast showing taskpaper and annotation possibilities with papers2 for a recent course ((sorry, in portuguese). With skim it has become even easier.

    Thanks for your site. It is great!

    Dr. Mauro Gracitelli
    CRM 113008
    Cirurgia do Ombro e Cotovelo. Traumatologia
    Grupo de Ombro IOT-HCFMUSP


  3. Pingback: Writing Workflows: Processing Annotations (All Roads Lead to Skim) - Jeff Taekman's WiPPP

  4. Like Mauro, I use Skim as a hub for PDF annotations and then export my notes elsewhere. I export all of my notes into Markdown plain text and then translate that into HTML that I “host” in my Evernote. I have written an extensive Applescript that exports all of my Skim notes, organizes them into Sections, formats them for Markdown, and embeds hyperlinks back to the individual pages of the source PDF (if you use my custom URL scheme or DEVONthink).
    For anyone interested, you can find my script and detailed descriptions and instructions (as well as a good bit of others scripts and tricks) at my blog:



  5. Pingback: 文獻回顧資料整理方法 Literature Review in Mac — Papers, TaskPaper, DEVONThink Pro/Evernote | Li-Wei's Mac in Academia

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