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:
- How to annotate PDFs on various platforms
- 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.
I 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.
Once 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.
Now 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.
Clicking 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.
Bookends 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.
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.
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.
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.
Once I’ve made my annotations, I tap the export icon in the top right-hand corner and then tap “Send by Email.”
An 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.
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.
I can also open Bookends to make sure the annotations made in PDF Expert 5 appear in the built-in PDF viewer.
Et 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.
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.
 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.
 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.
 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.
 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.