Working with PDF Annotations: Bookends, PDF Expert 5, & Evernote

Annotation is a vital part of academic reading and research. It’s a practice that is discipline- and field-agnostic—all of us need to mark up our texts as a way of interacting with what is being communicated to us. With physical documents (books, articles, etc.), this is as easy as grabbing a pen, pencil, highlighter, and/or some Post-its and annotating pages at will. Digital documents (ebooks, PDFs, etc.), on the other hand, can prove rather unwieldy when it comes to highlighting, underlining, and jotting in the margins, especially if you’re unfamiliar with the range of digital document viewers/editors available on desktop and mobile platforms. While such applications have made strides in annotation functionality over the past decade or so, a slight learning curve is still involved in even the most basic aspects of annotating PDFs from a laptop or tablet.

This post comes as a long overdue response to a couple of comments I received on past workflow tutorials about how I use PDF Expert 5 for iPad, Bookends for Mac, and Dropbox as a graduate student in the humanities. Both comments brought up the issue of working with annotations. From these comments, I’ve gathered that there are two fundamental elements to working with annotations in a digital environment:

  1. How to annotate PDFs on various platforms
  2. How to “free” annotations from their respective documents for further organization, manipulation, and cataloguing

The first element is solely a matter of technical knowledge, and in this post, I’ll briefly cover the annotation functionalities that are built into the devices and applications I use on a regular basis. As of this moment, these devices and applications are:

  • an early–2011 13“ MacBook Pro (my Air is no longer with us…RIP)
  • a 4th generation 16GB iPad
  • Bookends for Mac
  • PDF Expert 5 for iPad

The second element of digital text annotation (”freeing” your annotations for use elsewhere) also involves some technical knowledge—namely how to extract annotations from various applications. However, more importantly, this step requires an understanding of how you work as a reader, researcher, and writer in order to create a system that will automate, to a certain extent, the extraction, filing, and organization of your annotations. I’ll outline my current workflow and try to justify why I’ve chosen to set things up the way I have, but there should be enough information in this post to allow you to alter the workflow to best suit your own personal needs.

Although I’ve been annotating texts since before my undergrad years (I’ve never been squeamish about marking up the margins of books), I must admit that I’ve never been very keen on doing anything further with my annotations after they’ve been made. I don’t transfer them to notecards or a special notebook. I mostly use them as a way to visually identify the most important parts of a text when I’m flipping through the pages of a book or an article—parts of the text that will later make their way into a paper as citations. However, my thinking on annotations has recently changed, largely because I will begin working on my PhD this coming fall. I’ve witnessed the intensity of reading involved in preparing for doctoral comprehensive exams in my current graduate program. From what I’ve gathered, the process of identifying and then recalling the most important parts of a text seems to be one of the most crucial and difficult aspects of this preparation. Good annotation practices and organization would certainly increase the efficiency and ease of this process. I also know that my doctorate research will dwarf my master’s research in scope and depth, and as more and more scholarly articles and books are published in digital formats, annotating digital documents (and then managing those annotations) will continue to play a bigger and bigger role in my (and everyone else’s) reading and research. Thus, I figure having a solid system and workflow for PDF annotations from day one will only make things easier for me in the years to come.

Annotating PDFs using Bookends for Mac

When I began my master’s program in English, I started using Sonny Software’s Bookends to manage my reference library. In other posts, I detail the different ways I use Bookends to organize my references, attach full-text PDFs to these references, and sync these PDFs to Dropbox, which allows me to access them from my iPad for reading and annotating. As of version 12.2 of Bookends, users can now annotate PDFs from directly within Bookends’s built-in PDF viewer, which is fantastic for those who would prefer to manage, read, and annotate PDFs all from Bookends on a Mac. Version 12.2 also added PDF annotation integration with the note stream feature in Bookends, which now displays all text-based annotations (highlights, underlines, comments, notes, etc.) along with user-created note cards in the note stream panel for any PDF attachment. Here’s how it all works.

01-blank-pdf-Ezra-PoundI open Bookends on my Mac and start with a fresh, clean PDF of Ezra Pound’s “A Few Don’ts by an Imagiste,” courtesy of the Poetry Foundation’s website. I have the bottom pane in Bookends set to display the attachment and the right pane to display the note stream. As you can see, the note stream is initially empty.

In order to include all annotations in the note stream (and not just Bookends-specific notecards), I need to first check “Show Highlighted PDF Text as Notecards” in the attachments options menu, which can be accessed by clicking the cog button at the top right of the bottom pane. I have also chosen to check “Show PDF Note Modification Date in Notecards” because it seems like a nice extra piece of information to have.

02-show-annotations-note-streamOnce those options are set, I select a bit of text with my cursor, open the attachments option menu again, and click “Highlight Selected Text.” You can also use keyboard shortcut “control+option+H” to eliminate the second two steps and save yourself a bit of time.

03-highlight-selected-textAs soon as the text is highlighted, it appears in the note stream in the right pane.

04-highlight-in-notestreamNow that the annotation is part of this attachment’s note stream, we can choose to create a Bookends-specific notecard containing the highlighted text by right clicking on the entry in the note stream.

05-convert-highlight-notecardClicking the “Add the Selected PDF Annotation and Page # to Bookends” creates a new Bookends notecard containing the highlighted text along with the page number on which that highlighted text appears.

06-highlight-and-notecardBookends notecards are stored in the Bookends library database, not the PDF itself, so you’ll only be able to see these types of annotations in the Bookends app.1 Note that if an annotation entry in the note stream has a small lock icon in the upper left-hand corner, it means that its text cannot be edited—in other words, it is likely highlighted text and Bookends therefore treats it as more of a “virtual” notecard. To edit a locked entry in the note stream, you’ll have to right click it and add it to Bookends using the process I just explained.

There are two other annotation features built into Bookends: inline notes and comments. The steps for creating both of these types of annotations are generally the same. First, open the annotations options menu by clicking the button with the cog icon. Next, click either “Make Comment” or “Make Note” and then click the spot on the PDF itself where you would like to insert the inline comment or note. Finally, enter your text.

Adding a new note.

Adding a new note.

Adding a new comment.

Adding a new comment.

Comments are always visible as text on top of the PDF itself, while notes appear as small notepad icons that the user must click to expand and view. Another key difference between the two is that comments do not appear in the note stream, while notes do.

09-comment-pdfFinally, just to see how annotations made in the Bookends built-in PDF viewer translate to another PDF viewing application, I’ll open the recently annotated Pound article in Preview for Mac.


All highlights, notes, and comments are visible. I didn’t test any other PDF applications (i.e. Adobe Acrobat or Skim), but I would imagine that they would behave in a similar fashion.

Annotating PDFs with & Extracting Annotations from PDF Expert 5 for iPad

Despite having recently purchased GoodReader on sale to have a look at what the latest version of the app offers, PDF Expert 5 remains my primary PDF-related app for iOS.2 The app’s interface is clean and easy to navigate, and it provides all the tools necessary for viewing, annotating, and organizing PDFs both locally from the iPad’s storage and remotely from cloud services like Dropbox or Google Drive.

As I mentioned at the beginning of this post, one of the challenges with PDF annotation is freeing or extracting highlights, underlines, notes, and comments in a PDF for further organization or manipulation in other applications. PDF Expert 5’s solution to this challenge is a simple annotation export that inserts a raw text summary of all annotations from any PDF into the body of an email and also attaches the full PDF file to that same email.3

To give a brief demonstration of this feature, I’ve downloaded the Pound article from earlier onto my onto my local iPad storage through PDF Expert.

12-pdf-expert-poundIt’s worth noting that all of the earlier highlights, notes, and comments from Bookends are visible in PDF Expert.

I’ll go ahead and add a few more annotations in PDF Expert before exporting the raw text summary. As I will later demonstrate, all annotations made in PDF Expert will also be visible in the Bookends internal PDF viewer.

Adding a note.

Adding a note.

Adding a comment with border.

Adding a comment with border.

Once I’ve made my annotations, I tap the export icon in the top right-hand corner and then tap “Send by Email.”

16-pdf-expert-shareA “Choose the file format” dialogue will appear. We want to select the third option: “Annotations Summary.”

17-pdf-expert-email-dialogueAn email window will then appear with the raw text summary of all text-based annotations.4 The PDF file itself will also be attached to the email, as indicated at the bottom of the email.


Sending PDF Annotations to Evernote

This is where you can get creative with your workflow. For now, I’ve chosen to use Evernote as my repository for annotation summaries. Thus, in addition to sending this annotations summary to my personal email address, I’ve chosen to send it to my Evernote email address.

19-pdf-expert-send-to-evernoteAs a result, Evernote creates a new note in my default notebook with the annotations summary text as well as the PDF attachment.

Evernote's text summary of the PDF annotations.

Evernote’s text summary of the PDF annotations.

First page of the PDF attached to the Evernote note.

First page of the PDF attached to the Evernote note.

Second page of the PDF attached to the Evernote note.

Second page of the PDF attached to the Evernote note.

Before I leave my iPad, I upload the recently annotated Pound article back to my Dropbox to ensure that Bookends will have access to the latest version of the text.


Back to the Mac

When I return to my Mac, I can view the annotations summary in my email.

24-email-annotations-summaryI can also open Bookends to make sure the annotations made in PDF Expert 5 appear in the built-in PDF viewer.
25-bookends-notestream-updatedEt voilà: the annotations are visible in the PDF text itself as well as in the note stream panel to the right. Just for the hell of it, let’s see how they look in Preview.

First page of the updated PDF in Preview.

First page of the updated PDF in Preview.

Second page of the updated PDF in Preview.

Second page of the updated PDF in Preview.

Looks good to me.

For me, the most powerful and flexible piece of this workflow is the annotations summary text email in PDF Expert 5. While email might seem like an archaic technology when compared with things like cloud storage, mobile applications, and the like, its power lies in its versatility. I’ve given only one example of this versatility in showing how one might leverage Evernote’s email integration to automate one of the steps involved in filing and organizing annotations. There are numerous other applications that implement a similar type of email integration (i.e. giving the user a unique email address used specifically to add items to his/her account) if Evernote doesn’t suit you.5 Another option I’ve entertained would involve creating a new email account (most likely Gmail) dedicated solely to storing annotations summaries. The email client would then act as a kind of filing system, each email serving as a hybrid text/PDF file containing a summary of annotations and the original full-text article. Basic features like folders and tags could be used to manage and organize annotations. Additionally, Gmail’s search capabilities would prove invaluable for a large collection of annotations, and working with raw text would allow for export of data at anytime if necessary.

I could go on, but the point should be somewhat clear by now. The combination of Bookends for Mac with a solid PDF app for iPad (or any mobile device, for that matter) makes it easy to work with digital document annotations in a variety of ways. I’m sure my own workflow will transform and evolve over time, but I believe that the fundamental structure and order of how annotations are made, exported, and filed will remain generally the same for quite some time.

[1] Bookends notecards text is also visible in the Bookends on Tap iOS app.

[2] The latest iteration of GoodReader has a lot to offer. However, I still find the user interface rather cluttered and chaotic. I believe GoodReader provides some features that PDF Expert 5 does not (such as a wider range of file type compatibility and integration with more external storage sources), but none of them have sold me on making the switch to GoodReader. That said, I would definitely recommend taking a good look at both apps before you choose one over the other.

[3] Ok, so, I’m kind of going to contradict what I just said in the previous footnote. One minor advantage that GoodReader has over PDF Expert 5 is that it allows its users to export a raw text summary of all annotations contained within a PDF with or without automatically attaching the PDF itself to the email. PDF Expert 5 will always automatically attach a copy of the PDF to the email. While you can easily remove the attachment from the email before sending it, it’s still an extra manual step to factor into the workflow. Perhaps I’ll send a feature request to the people at Readdle.

[4] By “text-based annotations,” I mean annotations that interact directly with the existing text in the PDF or add plain text to the PDF. In other words, “drawn” annotations, such as circles, squares, lines, arrows, and free-hand underlines/highlights, will not be noted in the annotations summary. While I’m sure this could be programmed into the export, it likely is not because “page 1: circle” would pretty much be useless information when scanning a summary of annotations. What this also means is that in order to make use of highlights and underlines that will be exportable to the PDF annotations summary, the PDF being annotated must contain text that has been optical character recognized (OCRed). Most PDFs from scholarly journals will be OCRed, allowing you to interact (i.e. copy, paste, search, etc.) with the text as text rather than as an image. However, you will inevitably encounter non-OCRed PDFs. In this case, only text notes/comments that you add to the document will appear in the exported annotations summary. I use ABBYY FineReader to OCR any scans I make of physical texts or PDFs I download that are not already OCRed. It’s a tad pricy, but there’s a student discount. There’s really no comparison between working with a rich OCRed PDF and a flat image-based PDF, so I’d certainly say FineReader’s price tag is worth it.

[5] Simplenote used to offer a premium feature like Evernote’s for adding notes via a unique user email address. Since discontinuing its premium service, however, Simplenote no longer offers this feature, though I’m certain there exist other similar notes applications that do. If you know of any good ones, I’d love to hear about them.

8 Comments Working with PDF Annotations: Bookends, PDF Expert 5, & Evernote

  1. Kathy Love

    Ben, just wanted to say a huge thank you. I am struggling at the moment with the problem of how to manage a wide range of material , some digital, some hard-copy, together with notes and annotations. I use PDF Expert and Dropbox, but had never thought of things like Bookends and Evernotes. I am a lawyer, now doing a large project in legal history, so I have a range of articles, books and original sources to work with. Your clear descriptions of what you do, and why, and exactly how, have been a tremendous help! Many thanks, and best wishes,

    1. Ben Lee Taylor


      Thank you for the kind words! I’m glad my articles (which I feel can be a bit long-winded and overly detailed at times) could help. Best of luck with your research project, and thanks for reading.

      1. Kathy Love

        Ben, you have no idea how useful that level of detail is! Especially for those of us with no natural affinity for electronics.
        But you’ve got me thinking. Did you ever look at DevonThink? I work increasingly with original medieval sources which I can’t copy, and aren’t in pdf form, so I just have to take notes (in Word for Mac). I know I could save each Word document as a pdf, but that’a a pain and it would be great to find an indexing tool that could handle different formats.
        Would be very interested in any thoughts you have—if you have time at all, in the light of your own PhD!
        In any case, really appreciate the help you’ve already given to a lot of us!

      2. Ben Lee Taylor


        I actually did try to use DEVONthink before settling on my current workflow. While it’s a very powerful tool for organization, I found that it complicated things for me rather than simplifying them. I can’t remember any specific issues I had (this was almost two years ago now), but I felt a bit overwhelmed when trying to decide how many databases to use and what level of depth to give my organization (I have a tendency to overuse subfolders). These problems may have stemmed from the fact that I was trying to use DEVONthink to organize my entire life (from school work, to bills, to photos, to blog posts) rather than a single project or aspect of my life. I also wanted to continue using Bookends but still have access to my academic sources through DEVONthink. This required indexing my Bookends attachments folder rather than importing it to DEVONthink, and at the end of the day, it started to seem like I was just using DEVONthink as an alternative to Finder, which seemed like overkill for what I needed. I ended up deciding that I would make an effort to get better at using some of Finder’s more advanced organizational features, such as tagging and saving advanced searches for later use.

        In any case, I do think DEVONthink is a very powerful tool and might work for you if you know in advance what you specifically need it for. Again, when I used DEVONthink, I think I may have expected it to magically tell me how I should organize my digital life. While the app might help with that, there’s still an element of preference and design that the human user must provide.

        Also, it might be worth mentioning that Bookends does handle multiple different formats as attachments. What I haven’t looked into, however, is the app’s ability to index the contents of those attachments—i.e. allow for searching inside the text of OCRed PDFs, Word/text documents, etc. Spotlight and Finder can certainly do this, so you could just use Bookends to manage and organize your research library and use Finder to search within specific attachments when necessary, but then you might end up doing a lot of switching back and forth between Bookends and Finder.

        Sorry I don’t have a definitive answer to your question, but hopefully something I said sparks an idea.

      3. Kathy Love

        Ben, how kind of you to take the time to reply so fully and helpfully. I think you put your finger right on the two problems I keep tripping over: one, how to design a system that doesn’t require translating stuff from one app into another all the time; and two, how to structure a large assortment of data in a way that allows you to see each piece in the context of the whole without losing access to the detail.

        I had almost decided to go with DevonThink and try to use tags to organise things, but this weekend two friends came to stay, both medieval history dons who both research and teach, so I asked them what they did about all this. Their answer surprised me, and I offer it just as a different approach that might be interesting to know about.

        They use Excel to organise everything, and require their students to do so too. Their advice was to draw up a spreadsheet with a separate column for each element that you may want to refer to. (These will vary by topic, but as a lawyer I might use date, source name, page or manuscript, court, name of judge, names of parties, nature of legal claim, details of related litigation, etc.) Excel allows you to pull out these elements, or any combination of them, and to filter, rank or match them (horizontally or vertically) according to various criteria, so you can look for patterns, correlations and gaps. It is particularly helpful if you intend to do any statistical analysis. This ability to select and manipulate data is (my friends said) the key to getting the best out of your data, both at the stage of developing your arguments and in the course of writing.

        They real trick to this is that your choice of elements sets the overall analytical matrix that will govern the whole project. Of course you can modify it if necessary as you go, by adding new columns or collapsing existing ones, but that overall structure forces you to locate each datum in the overall matrix as you go along so you keep your eye on the main lines of argument and don’t get lost in detail. This does require you to enter data on the spreadsheet, but locating all significant data in an overall plan is an unavoidable step in any major piece of academic writing, and under this system you do it as you go.

        One further refinmenet. An Excel spreadsheet can only accommodate a very brief indication of the contents of each entry, but if in the spreadsheet you embed a link to the document (pdf or Word) holding the detailed info, you can give only a brief description or summary in the spreadsheet and click on the link to get the detail if you want it. This embedding is very easy to do (there are plenty of instructions on the web) and you can even set it to link to a specific place in the pdf or Word document, so by clicking on the link you go straight to the relevant point.

        I think this system will work for me, so I am in the process of setting it up. There is a hefty upfront load of getting my existing data in the spreadsheet, but by forcing me to look analytically at what I’ve already got, it is helping me see how my arguments are developing, and what gaps in my research need to be addressed.

        This may not be of any interest, Ben, but I liked the idea of being able to do so much with a programme that is well-known and very stable, and at least it might be a useful approach to know about.

        Thanks again for all the things you write. It is incredibly helpful to hear the ideas of people who are wrestling with the same practical issues that I am, but who know so much more about the available solutions!

        All the very best,

      4. Ben Lee Taylor


        I have to admit that I was a bit skeptical about your comment when I read the first mention of Excel (probably similar to the surprise you initially had at your colleagues’ suggestion). However, after reading through, I think it sounds like an excellent solution to the two challenges you mention in the first paragraph.

        I think my skepticism is primarily a result of my lack of knowledge and experience with Excel. I know the basics well, and I can work with more advanced formulas and functions if necessary (which always requires some Googling), but I haven’t worked with the software enough to where it feels natural (if that makes sense). I love the idea of embedding links, though. I often have a simple text document or physical notepad (I still enjoy pen and paper every now and then) with a list of important citations and page numbers that becomes unwieldy at a certain point. I’m not yet sure if the work would be worth the payoff, but it might be worth transferring these lists into a spreadsheet, in which I could, as you mention, embed links to the PDFs I reference. Similar to the way in which you would set up columns for name of judge, name of parties, nature of legal claims, etc., I might tag citations by author, relation to theory or criticism, relation to a character in a novel, and so on. And again, as you’ve pointed out, once these columns are created and loaded with data, Excel allows you to manipulate this data in a number of ways to better visualize and analyze your research.

        I really appreciate this dialogue, as I’ve found (in my limited experience) that scholars (especially those in the humanities) focus very little attention on the tools we use for research. I think better understanding these tools can help increase the efficiency, organization, and (ultimately) quality of research. It also helps that I really enjoy tinkering around with this kind of stuff.

        Anyhow, best of wishes to you in your research and work, and the next time you speak with the two colleagues you mentioned in your comment, please give them my thanks for sharing their ideas on this topic.

  2. Roy

    Hey Ben,

    Thanks for publishing this & updating it. I’ve been working on finding a more functional and streamlined system than the one I have been using and your post has helped me settle on bookends. Anyway, evernote is now requiring a plus or premium account for the emailing feature & I just wanted to plug sendtodropbox as a workable alternate. When I email from PDF Expert into my sendtodropbox account, it creates a text file with my highlights and comments from the pdf. I can then sort using spotlight and just cut & paste the plain text into a word doc. I’d like to automate the process but so far that’s a bit beyond my skill set. Anyway, thanks for sharing your workflow!

    1. Ben Lee Taylor


      I’m just now getting around to replying to a couple comments after a hectic holiday season. Thank you for the kind words and for the sendtodropbox suggestion. I’m not familiar with the service, but I like the idea of using PDF Expert’s built-in email functionality alongside sendtodropbox to extract annotations and get them synced to Dropbox in one go. I have been neglecting my site for too long, but I’ve made quite a few adjustments to my workflow and will be posting some new articles soon!


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