Tools for school – Digital document annotation on an iPad, iPod Touch, or laptop

[FYI, this post also has been translated into Croatian by the WHGeeks Science section!]

[Warning: this is a long post. Cross-posted at LeaderTalk.]

I’ve been playing around with digital document annotation on various portable computing devices. Here is an overview of where I am right now…

The old way!

First of all, just as a reminder, the image below is the way that we’ve traditionally annotated ink on paper. Some of you like to use pencils or pens to underline, write notes in the margins, etc. In my life I’ve spent a small fortune on yellow highlighters.


Kindle App for the iPad

Will Richardson got me thinking with his post on using the Kindle app, his iPhone, and Evernote together for document annotation and sharing. So I decided to try it myself with the Kindle app. I don’t have an iPhone, but I do have an iPad and two iPod Touches.

Here is what it looks like when you press and hold on a word to begin your highlight (or note) in the Kindle app for the iPad:


Once the word is selected, you can push and drag on either of the dots to resize the selection and cover more text. Note that the magnifying box helps you see where you are.


Once you’ve got your text selected, you click on Highlight or Note and it gets saved with your document. Repeat as desired.

Kindle App for the iPod Touch (or iPhone)

The process is the same for the Kindle App for the iPod Touch (or iPhone). Here are two images that show you what it looks like on the smaller screen. Again, note the draggable dots as well as the magnifying box.


Kindle App for the PC

The Kindle App for the PC essentially works the same way. Use your mouse to click and drag, selecting the text you want in a highlight or note. When you’re done, select the option you want from the popup box. The gray text background then turns to yellow. See in the image below that the Notes & Marks button is selected at the top right, allowing me to see all of my notes and highlights in a scrollable list on the right.


Note: The text you select in the Kindle App for the PC is NOT copyable for future pasting into another document.

Your notes online: Why this is better than marking up ink on paper

So far, so good. The process basically works like a traditional highlighter. Every time I sync the Kindle app with Amazon’s server, my notes and highlights show up on all of my other devices too. I don’t have to lug multiple, heavy books around. I can just carry my ultralight laptop, my svelte iPad, or my pocket-size iPod Touch and have access to my reading and the accompanying highlights / notes.

As Will noted in his post, the beauty of all of this, however, is that Amazon also makes available a web site where you can see all of your Kindle notes and highlights. I can even see an aggregation of others’ highlights if I wish (which is pretty cool).


The text on the web site is selectable, which means you can copy and paste it into other applications. For example, you could put all of your highlights into a Word document, a blog post, or a note in Evernote. Will did the latter, and I’ll walk you through that process…

Using Evernote to publicly share your notes

Here’s what it looks like in Evernote if you just copy-and-paste directly into a new note:


If you clean it up first – using some judicious search-and-replace – then it can look more like this:


You can share your notes and highlights with others by making a public notebook (or tag) in Evernote. In the image below, I’ve right-clicked on the notebook I want to share and then selected Properties.


A popup box appears. Click on Sharing and collaboration options:


The Web version of Evernote launches and you get to choose if you want to share with individuals or the world at large:


If you start sharing with the world, you get a personalized URL to which you can send others (e.g., They can click on the appropriate note and see everything you’ve put in the now-public notebook. Pretty nifty!


Another alternative: iAnnotate PDF

In addition to doing what Will did, I’ve also been experimenting with the iAnnotate PDF app for the iPad. I wanted a way to edit dissertation drafts, online reports and white papers, and other documents in PDF format. Although the GoodReader app (and, maybe soon, the iBooks app?) works great for viewing PDF files, you can’t edit them within the app. I read good things about iAnnotate and decided to try it.

I had some initial trouble getting documents into iAnnotate. I finally figured out, however, that the best way to do it is to synchronize it with a DropBox folder. That works pretty well (for GoodReader too!). Once you open a PDF file within iAnnotate, you have a number of tools at your disposal, including the ability to highlight, underline, strike out text, draw freehand, and leave yourself a pop-up note:


Although iAnnotate doesn’t give you the option of synchronizing to a web page like the Kindle app does, it does let you e-mail your annotations (with or without the document). When the annotation summary is received as an e-mail, it looks like this:


That text is then selectable, which means you can cut and paste it into other applications. Managing documents within iAnnotate is very easy, just as it is for the Kindle apps.

Reflections and implications

Here are a few thoughts:

  • The possibilities of all of this for academic work are endless. I will use the Kindle app to read nonfiction books like Clay Shirky’s Cognitive Surplus and capture the quotes and notes that I think are important. I’ll use iAnnotate PDF to do the same for those documents and research reports that I’m always digging up online. When my students send me their writing, I’ll quickly convert those documents to PDF and then be able to comfortably annotate anywhere on my iPad, without being tethered to my laptop or desktop computers. And so on…
  • I love having all of the text from a book or report that I think is important – and ONLY that text – in one place. It’s searchable, it’s editable, it’s MINE. No more flipping through pages trying to find something. No more using multiple bookmarks and Post-It flags. A quick search and the text I want is there.
  • It would be nice if you could cut and paste from the Kindle App (particularly the one for the PC) into other applications.
  • The Pogo Sketchup Stylus – a special stylus for the iPad, iPhone, or iPod Touch – is worth every penny when it comes to annotation. Highlighting text – particularly on the iPad – is a breeze compared to using my (apparently too fat) finger because the stylus has a smaller surface area and thus is more precise.


  • As digital annotation and sharing tools continue to become more robust, it becomes much more feasible to use iPads and other mobile computing devices as replacements for books and textbooks.
  • Like Will, I may never buy a nonfiction book on paper again (unless I have to).
  • I like Will’s idea of getting notes off of the Amazon web page and into Evernote. If iAnnote or the iBooks app or other e-book readers and annotation tools also make available online or e-mail versions of highlights and notes, I’ll do the same for those too. That way I won’t have to worry about particular proprietary formats becoming obsolete. Now, if Evernote ever goes out of style, I’m in big trouble!

So this is where I am right now with all of this. Although digital annotation using these tools is not yet as smooth as I would like, I’m deriving a lot of benefit from the new capabilities that I do have.

How about you? How are you annotating digital documents on portable computing devices? Got any tips or suggestions?

52 Responses to “Tools for school – Digital document annotation on an iPad, iPod Touch, or laptop”

  1. Without a doubt iAnnotate is the best reader and text mark up application, it is on both my iPad and iPod touch, synced because I use my computer as the “server”. The Kindle app is great for highlighting and adding notes for the books, of which I am now averaging two books a month, where I was reading very little before, in fact I am toying this on my iPad, and if I didn’t have to use SPSS my net book would be completely replaced. No laptop or desktop again for me, or my three year old son who is now the owner of my iPod touch.

  2. I should also add that GoDocs is amazing for working in the cloud, allowing you to edit, share and create documents via Google Docs.

  3. Really excited to play with iAnnotate. This looks like a great app to use for digitally grading. I have been struggling with good ways to teach annotation of PDFs with my faculty – this maybe the perfect option.

    I am a big fan of Evernote, it has been a game changer for my educational use of the iPad, looking forward to playing with it more, especially with using my Kindle notes.

  4. Great post, Scott. I am using the exact same strategy:

    – Kindle for general books
    – iAnnotate for journal articles and other PDF documents
    – Pogo stylus for highlighting within Kindle and iAnnotate (it’s a pleasure to use for general navigation on the iPad as well).
    – Dropbox to hold PDFs which are wirelessly moved from my Mac to iAnnotate via its wifi transfer utility (Note: use of Dropbox is not necessary for the transfer, but it adds a layer of accessibility to my reading docs from other platforms, which is nice. and until things become incrementally better, this is the best route for academic users of the iPad.

    iAnnotate needs to take one more step for academic users and integrate something elegant that lets one:
    – strip the citation of a journal article and put it in APA format
    – take the journal page number, not the PDF page number, and add it to the highlights a user makes (again, to facilitate easier APA style use of quotes). I will say, thought, that one way around this is for the user to not use direct quotes, but instead paraphrase passages.

    All in all I find myself reading much more now with this setup–both academic material and general content.

  5. Very interesting post! I hadn’t heard of Iannotate or Evernote so I will definitely try out those applications, if possible. I’ve been considering buying a tablet PC if I can find one that is good for drawing that supports Photoshop and Illustrator as well. I wonder if there is a good drawing app for the ipad that works with that pogo stylus because that would be very handy!

  6. Great post from you. I’ve been considering buying an ipad or any tablet pc but unfortunately ipad is not yet available in my location.

  7. Scott, thanks for the detail here. A solution I use for annotating on the PC is FoxIt Reader. Using Dropbox you could sync as you do for your files here. I’ve been trialling a few apps for iPod Touch and am yet to be find something that just works for me.

  8. Informative post. I’ve been exploring iPad PDF readers lately for use in teaching and presentations. iAnnotate, used as you described, is a compelling choice for markup. One feature is missing however…projection. For this, GoodReader (.99) is currently the best PDF reader with video out, though GoodReader lacks the markup that iAnnotate does so well. Perhaps markup with iAnnotate combined with the ability to share in GoodReader would be the right combination.

    Again, thanks for the work here. Highlighted this article in a post on my blog about the iPad.

  9. Thanks for the information, Scott. I recently acquired an IPad as part of a pilot program for my college, but I honestly didn’t know what to do with it (besides facebook and blogging, haha). I will search for some apps and let the fun begin!

  10. I’ve just spent quite a few frustrating hours trying to get my PDFs into iAnnotate. They are in DropBox, but how do I get them over to iAnnotate?

    Thanks for the full review.

    • Hi Sandra,

      It was frustrating to me too. It’s not exactly intuitive. You have to open and point the “Aji Reader Service” to your Dropbox folder. THEN, the Aji Reader Service has to be open and running on your computer in order for the iPad to find your files.

      Instructions and information are here:

      Good luck. Let me know how it goes!

      P.S. GoodReader is much easier – it seamlessly integrates with Dropbox. However, it doesn’t support annotation. Ugh.

  11. You can drag and drop them through iTunes no need tonmake it harder than if you have to.

  12. Drag and drop them through iTunes. As you can see I can’t type perfect on the iPad quite yet. Apologies for the double post.

    • Okay, now I have something to learn! Dave, how do you get the PDFs through iTunes and then into iAnnotate?

      • Hi Scott,

        I will try and do this without screen shots, it is pretty simple, but not highly advertised.

        1. Connect your iPad to the computer.
        2. Go into iTunes
        3. Click on the “Apps” tab
        4. Scroll down to where it says “File Sharing”, which is about towards the end when you scroll down.
        5. Click on the iAnnotate App (All the apps that have file sharing are listed here, so I have iAnnotate, Davinci, Pages, Quickoffice)
        6. Click the “Add” button (which shows up on towards the bottom right of the right hand pane)
        7. Find your file and click “open”
        8. Its Added to your iPad!

        It isn’t highly advertised, so I am not sure why it isn’t, as otherwise you end up trying to find very roundabout ways to get the job done. I find this drag and drop (actually not really drag and drop, but close enough!) to be the easiest. Plus you can do multiple files at a time.

  13. Thanks so much for that! I would ammend it only slightly to read:

    1. Connect your iPad to the computer.
    2. Open iTunes
    3. Click on iPad (under DEVICES)
    3. Click on the iPad “Apps” tab.
    4. Scroll down to where it says “File Sharing”, which is about towards the end when you scroll down.
    5. Click on the iAnnotate App (All the apps that have file sharing are listed here, so I have iAnnotate, Davinci, Pages, Quickoffice)
    6. Click the “Add” button (which shows up on towards the bottom right of the right hand pane)
    7. Find your file and click “open”
    8. Its Added to your iPad!

    Mystery solved!!!

    I should also add that I discovered that another easy way to get files into iAnnotate is through Papers:

    Arrow at top right, click Open In … iAnnotate Pdf. Papers costs $15, and iTunes is free, so this would only make sense if you already use Papers.

    I have my doubts about iAnnotate. If you can’t save and export your Annotations, or search them, what’s the point? Is there something I don’t know?

  14. Scott,

    I am able to email it to myself and see the mark ups, annotations, notes, etc as least when I open them in iAnnotate.

    To do this I open them up in iAnnotate. I then select another tab and another PDF, and then when I select back to the PDF I just opened, they are all there. This maybe a bug or maybe the way it works, but it works for me. I will email you a marked up document just to make sure it isn’t saving it locally on my iPad and pulling that information.

    When I open it in gmail via google docs I can’t see the markups, but when opened in the Adobe PDF reader, I can see them.

  15. When I say email, I mean email directly out of iAnnotate.

  16. Thank you — you’re right, Dave. Emailing the annotated document worked, and opened in Adobe Reader without any problem. Bravo!

    Given this, it should be possible to email ammended documents back and forth etc.

  17. Hi all! I just have a question about reading the annotated PDFs – once annotated in iAnnotate, can the PDFs be opened in a standard PDF reader and retain the mark up?

  18. Yes, absolutely. When you mark them up with iAnnotate they are annotated in regular Adobe PDF viewer.

  19. What other app do you need in order to edit docs? I am trying to use the ipad out in the field and I want to be able to view pdf plans and make notes AND be able to make changes to a word document if need be. Do I need something else besides Iannotate and dropbox? I was thinking about using godocs but thought that was a little too much going on for something like this! thanks!!

    • I use quickoffice because when I am on wifi I can take the document from the googledocs cloud and bring it local to my iPad on the go, edi tit on the go and then when i get back to wifi, I just sync it up to the cloud.

    • You can also use Docstogo which enables you to make changes in word, excel and ppt and have them reflected in the original docs on your pc when you syns

  20. I am curious, what percent of your time are you using your iPad when compared to all your electronics.

    Personally I use the iPad about 90% of the time. The only time I have used my net book since getting my iPad is for writin long papers and running SPSS. Anyone else offend they are moving towards iPad only?

  21. This is a great discussion — very helpful. I summarized what I’ve learned here, on iPad as an indispensable research tool:

    Corrections and suggestions welcome.

    Sandra Gulland

  22. Hi all,

    Great to have found the site, as I am a lecturer/grad student and have been struggling with many of the same annotation/sync issues. I have not tried Dropbox but am using Sugarsync with good results (good in the sense it offers a feasible workaround for iPad’s horrible file management system). Setup was easy and they have 2GB storage free, plus their folder system looks just like the one on my Mac (another blog suggests Dropbox is different and a single folder?).

    I have many PDFs marked up in Preview on my Mac but when opened in Sugarsync or Goodreader all annotations are missing. From Sugarsync, however, when I “Open in” to iAnnotate the markup and notes made in Preview reappear (except boxes). I can annotate and then email via Sugarsync’s “Upload by email” (they give you a special, personalized email).

    There is, unfortunately, a step where one must go to Sugarsync’s online file manager, open the emailed iAnnotated PDF (found under “Magic Briefcase” after some searching), and “Move” it to the desired folder or subfolder. It is then almost instantly synced to my Mac. Easy, but not intuitive for new users.

    I just did a test and the free-write/pencil/whatever-you-call-it is retained as well as all other annotations when I open in Preview.

    Pretty slick, and Sugarsync removed my angst that my daughter might inadvertently delete iAnnotate (or Pages or Docs to Go) and I would lose all my work that I hadn’t transferred over (why, Steve J., did you not include password protect for deleting, and why save files “in” the app?).

    Just wanted to share a little good news amid ongoing frustration with many iPad OS design features, and wifi connection drops, and…).


  23. Do I understand correctly that you can put pdf on the ipad using a usb cable and itunes but that you cant reload them back to your pc doing the same thing?

  24. Great article. I use iAnnotate as well in my PDF annotation workflow. Here’s my write up of it.

  25. i just got iannotate for my new iPad. It works fine except it will not highlight. every other function works: underlining, drawing, notes, bookmarks, etc. But the main reason i bought it is highlighting. It seems like it is “trying” to highlight because after i try to highlight text the “done” box appears, but no highlight appears. Any ideas?

    • Patrick,
      The specific PDFs you are trying to highlight are likely only scanned images of a document and they don’t actually contain the text of your document. Try saving a Word or Pages doc as a PDF, import to iAnnotate, and see if you can highlight.
      Good luck,
      Jeff Andrews

  26. There’s just one problem with these tools: because Kindle books don’t have pages, one can’t generate footnotes to the paper edition of the same book. For academic disciplines where we cite quotations down to the page number, these tools’ inability to replicate that citation structure limits their usefulness.

    • Shane, Kindle books give you a location number. Use that just like you would a page number. It works great.

      • Relying on Kindle location numbers would be fine if I could assume that all my colleagues have, and will continue to have, access to the book I’m citing in its Kindle format. But many of them, even in an era of ebooks, will be using university libraries which contain print copies of the same works. If I were to use and cite Kindle versions, I’d be making it much more difficult for others to factcheck my work (or to find the same source I used without buying a Kindle copy.) For me, that’s a major limitation.

        • Why would the inconvenience for someone who didn’t have the Kindle version be any different than the inconvenience for someone who didn’t have the paper version (or the microfiche version or…)? Either way, you have to track down the correct version (paper, Kindle, microfiche, whatever) and then find the location within, no? I guess I don’t see it…

      • I teach college classes, and have students wanting to cite eBooks. The lack of page numbers is always an issue for them.

        Per APA guidelines, Kindle location numbers are not to be used. When there is no physical page number, you treat it like any other doc that doesn’t have pages and include chapter and paragraph. However, the reference does need to list that it is an ebook.

        I hear the newer Kindles have an option to show physical page numbers. Would be nice for book clubs to have this feature. 🙂

  27. This is a great way of how you can share notes, highlights and real world ed uses. One thing as well is that iBooks does allow you to note and highlight text, downside being I haven’t found a way to collect them all in one place like amazon does nor email them. Apple does that or finds a better solution, it’ll be interesting.

    This is great though and would definitely come in handy for some profs I know and other educators.

  28. I have an iPad and a new kindle 3

    Synch works from kindle to iPad but the other way round kindle does not receive bookmarks or the last page read. So if I read furthest on the kindle the kindle app on the iPad knows and updates. But if I read furthest on the iPad when i synch the same book on the kindle it doesn’t know – it always says i am at the furthest location. But I am not. help! Anyone got any ideas?

  29. Hi, I have questions about iAnnotate:

    1) Are comments and markups saved in the pdf itself as part of the document, or do they only “exist” within the application like that?

    2) How do you save the pdf on the ipad? I don’t have one, but have heard that file management on the ipad is very tricky.


  30. Good afternoon,

    They are saved as part of the PDF so when you send them anyone with any type of PDF reader will see your mark ups.

    The file management with iAnnotate application in iTunes is very easy. You just drag and drop them from or to your iPad. In addition you can always open up PDFs that are mailed to you or you can download them direct from any website into iAnnotate. It is by far the most used and useful app I have as I work on my PhD.


  31. Dave, how do you download PDFs from a website into iAnnotate?


    Sandra Gulland

  32. Hi Sandra,

    When you open up the iAnnotate app on your ipad, hit the down arrow button, select web download, and then enter the URL of the PDF directly, or browse for the pdf file.

    I like to have the URL already copied, then I hit the down arrow, web download, and then past the URL into the URL spot.

    You can try it by following the above instructions, going to google, and then just google “PDF” and on the first results page you get some pdf files, and you can just hit the link and it downloads it to your ipad.

    Hope that helps.

  33. Thank you, Dave — that worked beautifully, the Memoirs of Saint-Simon downloaded to iAnnotate in a snap!

  34. To annotate PDF files I use Goodreader (0.99). A few updates ago annotation functions were added (e.g. highlight, add notes, draw shapes etc.). These annotations can be viewed and edited in other programs on the desktop (like the Mac preview).
    Tap and hold while viewing will reveal the options.

  35. Alex, is it possible to save only your annotations? From what I can see in Goodreader, you only have the option of saving the entire document with the annotations. I like that with iAnnotate I can save only my annotations (my highlighted passages).

  36. Scott,

    Great post. Is it possible to use iAnnotate with Google Docs? I don’t want to get Dropbox or try storage solutions unless it is really necessary.

    I got here looking for an annotation app for the iPad but I am hooked on your other posts too. I have just volunteered for my school district’s technology committee and your site is a wonderful read.



  37. Yes, but: the highlighting goes to ONE LETTER ONLY OR A FRAGMENT OF A WORD too?. Because I use to “transform” the text to make my own summarization, using even fragments of the text.

  38. Miguel,

    Scanned PDF documents don’t highlight with one highlighter in iAnnotate, so you have to switch to the freehand one. This of course means you can’t export summaries, etc.

    For most other PDF’s (have run across a few where you can’t highlight in sequence on the page), iAnnotate works perfectly.

    In my PhD program for example, sometimes I just highlight all text, copy and paste to word, and then save as PDF so I can make sure to use the highlights that provide summaries.

    • Thanks for answering.
      The scanned version of documents, of course, have the limitations you say: the highlights are only marks that can be processed later. But that is not an issue for me.
      The thing is that you might be ASSUMING that the selection, copy and paste of words -which many tablets do just fine in PDF readers, Word clones, etc.- does apply to FRAGMENTS OF WORDS too (Palms, for example, have that capacity in their programs and in the sensitivity of the screen, but ALMOST ALL tablets with resistive screen I have tried either does not have programs that can select parts of words OR does not have screens with enough sensitivity).
      Are you sure you have done it with your iPad? Would you please -if you have the time and the desire, of course- try to do it in your iPad and tell me if it can be done? (because I need a tablet that do precisely that).
      Thanks in advance.

  39. Hi Miguel,

    I use iAnnotate only on my ipad, never on a desktop/other device.

    Just to make sure I understand the question, are you asking if it is full highlighting? I would be happy to send three different highlighted PDF’s to you so you can see the difference (one scanned, one “regular” where text can be selected, and one where I put the text into word and then saved as PDF). In addition, those last two (not the scanned one) I would send what iAnnotate calls a “summary” for you to your email. You can email me at if you would like me to send them your way.

    I have been using iAnnotate since the iPad first came out, and personally would recommend it to anyone.

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