Using Bookends, PDF Expert 5, & Dropbox to Manage a PDF Research Library

When I started my master’s program at UdeM (Université de Montréal) this past fall, I decided that I would try to stay a bit more organized than I had during my undergraduate years. Aside from making better use of my time, trying to establish certain routines, and sticking to set task lists for the day, week, month, etc., I’ve tried to develop certain workflows that utilize technology to make my life a bit easier and less chaotic. One such workflow that I’ve really come to rely on involves the management of my digital (and physical, to some extent) library of PDFs with the help of Bookends for OS X by Sonny Software, PDF Expert 5 for iPad by Readdle, and Dropbox.

Before I go any further, I should admit that I am, for the most part, an Apple user, my primary computing hardware being a Mid–2011 13″ MacBook Air, a 4th generation 16GB iPad, and a 16GB iPhone 5. Thus, aside from Dropbox (which is available on almost any desktop or mobile OS at this point), there is an obvious bias toward OS X and iOS apps in this article; however, these apps are merely utilities built on specific platforms. I’m fairly positive that you could find similar utilities on the platform of your choice (Windows, Android, Linux, etc.) and still follow the concept of the workflow I’m laying out here. Also, I should mention that I spent a lot of time doing my own research on various apps and methods of file/data management before settling on what I’m presenting here. In fact, I pieced together a lot of this workflow after reading blog posts and articles on the same subject,1 so I’d suggest that you take what works for you and leave what doesn’t.

Setting Up Bookends for OS X

As Sonny Software puts it, “Bookends is a full-featured and cost-effective bibliography, reference, and information management system for students and professionals.” I looked at, and even tried, quite a few academic reference management applications before settling on Bookends, and I have no regrets about doing so. I easily could go into detail about the features and functionality of Bookends and why I find it so useful, but for the purposes of this post, I’ll just say that it’s a fantastic piece of software. By default Bookends stores both data (the various information relating to each bibliographical reference that you add or import to the application) and file attachments (for example, the full text PDFs that correspond to individual bibliographical references) locally on your computer’s hard drive.

This is the standard view of a library in Bookends.

However, I have chosen to store my file attachments on Dropbox, allowing me the benefit of having access to these files both locally and in the cloud via Dropbox. To do this, simply open Bookends, navigate to Bookends » Preferences in the top toolbar, and change the “Default folder” under “Attachments” to a folder within your local Dropbox folder.

Change the default attachments folder in Bookends » Preferences.

As you can see, I’ve created a folder named “Bookends” in my Dropbox root folder with a subfolder named “Attachments” where all my attachments are stored. As a side note, each time you add an attachment to Bookends, you can manually change the location to which the file will be moved or copied (instead of the default location), or you can choose to leave the file where it currently resides on your local hard drive. Simply choose “Move To” or “Copy To” in the first selection area, check the box next to this area (or leave it unchecked to leave the file where it currently is), and choose a folder location from the second selection area or click browse to choose a location not currently listed in this area (which, I believe, will list all subfolders of the default attachments folder).

Bookends allows you to override the default attachment location each time you add a new attachment.

Typically, I will download files (articles, papers, etc.) or scan physical documents to my Desktop or Downloads folder, attach them to their corresponding bibliographic references, and choose to have them renamed based on the title of the reference and moved to the “Attachments” folder in my Dropbox. As I mentioned, this allows me to view, edit, and usually download all of my attachments from any device with access to Dropbox.

Accessing, Viewing, Editing, and Syncing Bookends Attachments with PDF Expert 5

Similar to my experience with various reference management applications, it took me quite a while to settle on PDF Expert 5 as my iPad PDF viewer of choice. When I bought my first iPad, I used GoodReader for organizing and reading PDFs. However, I found the interface to be a bit dated, and with the release of iOS 7, GoodReader fell behind its competition.2 I started using PDF Expert in its version 4 days, and it served me well all through fall term classes. Readdle’s complete redesign of the app with the release of version 5 in December sealed the deal for me—I now use PDF Expert 5 for almost all PDF viewing and management on my iPad. Although not unique to PDF Expert 5 in terms of iPad PDF apps, I find the Dropbox integration and flow in PDF Expert 5 to be the simplest, most intuitive, and most useful of all the PDF apps I’ve tried. This is integral to my workflow with Bookends and the attachments that I store on my Dropbox. To set up Dropbox in PDF Expert 5, simply open the app and tap on “Dropbox” under “Accounts” in the left toolbar.

Once you’ve authenticated and linked Dropbox with PDF Expert 5, you should see it both in the left tool bar under “Accounts” and in the “Network” view.

Dropbox authentication should only take a few seconds, after which you will have complete access to the contents of your Dropbox account. If you set up your Bookends as outlined in the previous section, you should be able to navigate to your attachments folder and view all of your Bookends attachments.

I can view a list of all of my Bookends attachments from within PDF Expert’s file manager.

Tapping on any file will download that file in PDF Expert 5 and store the file on your iPad’s local storage. By default, PDF Expert 5 creates a Downloads folder in your Documents where all downloaded files are sent (this can be customized in the app’s settings).

By default, PDFs downloaded from Dropbox will be sent to a folder named Downloads.

Once you the file has downloaded, you can tap on it to open the PDF. This is where some of the more powerful aspects of PDF Expert 5 come into play, especially if you’re using the app for research reading. Using the toolbar at the top of the screen, you can add various annotations to the PDF. I’ve added a couple small annotations to a document to demonstrate how they will transfer when the PDF is uploaded back to Dropbox.

Highlighting text and adding a sticky note.

Highlighting text and adding a sticky note.

Finished product.

Finished product.

To do this, all you need to do is go back to your attachments folder in the Dropbox storage area of the app, tap “Edit” in the upper right hand corner, tap “Upload” on the left toolbar, navigate to the file you would like to upload, tap the file, tap “Upload” in the upper right hand corner of the pop-up menu, and tap “Replace” when prompted. The file should upload to Dropbox with its annotations, replacing the original, unannotated file.

09-pdf-expert-choose-file-upload

Choose the file to upload to Dropbox.

10-pdf-expert-replace-dropbox-file

Tap “Replace” when prompted.

Success!

Success!

Once the file has been successfully uploaded to Dropbox, I would advise that you delete it from PDF Expert’s local storage (as long as you don’t plan on annotating it again any time soon), as locally stored PDFs can quickly eat up valuable iPad storage.

Back to Bookends: Viewing Annotated PDFs in OS X

To wrap this up, the final element of this workflow is viewing the annotated PDF in OS X. I like to take as little to class with me as possible. Unless I have a physical copy of the reading for the day, all you’ll see in front of me is my MacBook Air and a thermos filled with hot coffee. Thus, it helps to have all of my readings with annotations accessible from OS X. Using the example of the Schiller text that I annotated with PDF Expert 5 in the previous section, let’s take a look at how the annotated PDFs make it back to home base (my laptop). Dropbox sync is almost instantaneous these days, so as soon as you upload an annotated or updated PDF from PDF Expert to Dropbox, you should see a notification in OS X that a file has been added to or updated in your Dropbox folder. Looking in Finder, I can see that Letters Upon The Aesthetic Education of Man was last updated today at 10:14, which is when I uploaded the annotated copy of the text from PDF Expert.

Check the modified date to be sure that you have the latest version of the file on your local hard drive.

Check the modified date to be sure that you have the latest version of the file on your local hard drive.

If I open the PDF in preview, I can view and even edit the annotations made in PDF Expert, which is very useful when viewing the PDF in class and wanting to add an additional note here and there.

All of the annotations made in PDF Expert now in Preview!

All of the annotations made in PDF Expert now in Preview!

Also, as far as I know, annotations added in Preview should show up in PDF Expert, were you to download the file once again from Dropbox within PDF Expert. Of course, an even easier way to access your Bookends attachments is from within the Bookends app itself. Using the search bar in the upper right hand corner, I can quickly search for “letters” to find the Schiller text. Because Bookends recognizes the attachment as existing in the attachments folder within my Dropbox folder, anytime a file is updated via Dropbox, its corresponding attachment in the Bookends app will be updated as well. You can quickly open Bookends attachments in Preview by double clicking them. Right clicking anywhere on the attachment will display other available actions, such as “Reveal Attachment in Finder.”

     Search for the bibliographic reference, click the Attachments tab on the right, and double click the document to open in Preview.


Search for the bibliographic reference, click the Attachments tab on the right, and double click the document to open in Preview.

So, there you have it—a relatively simple workflow that connects the OS X reference management app Bookends with the powerful iPad viewing, annotating, and management app PDF Expert 5 via the ever useful Dropbox cloud service. As a caveat, I feel that this way of doing things may be more conducive to disciplines within the humanities than those in other realms of study. However, even if you don’t follow this guide step by step, there may be bits and pieces worth implementing within your own reference and PDF management system.

[1] Here are a few of the blog posts and articles that I found most helpful in comparing and contrasting various reference management apps:

[2] While writing this, I took a look at GoodReader’s website and discovered that they recently released an update to their app with a complete redesign à la iOS 7. As much as I’d like to give the new app a try, I’ve invested too much time and energy into PDF Reader 5 to justify making another switch. However, I’d definitely suggest taking a look if this is your first venture into the world of PDF management on the iPad.

12 Comments Using Bookends, PDF Expert 5, & Dropbox to Manage a PDF Research Library

  1. luna

    thanks for the interesting article, Ben, also, writepdf is good for pdf annotation and printing etc. looking forward to more of your posts!

    Reply
  2. Hans

    Thanks for a good article! I’m considering switching from Papers to Bookends, and I wonder why you don’t mention the “Bookends on tap” iPad app? Is it just that you find PDF Expert superior to Bookends own app?

    Reply
    1. Ben Lee Taylor

      Hans,

      Apologies for my ridiculously late reply. It’s really hard to sift through so many spam comments to find real people, so I hope you get a notification from this reply.

      For reading and annotating PDFs, yes, I find PDF Expert far superior to the Bookends on Tap app. I do, however, use the Bookends on Tap iPhone and iPad apps to sync all the meta data of my research library. It’s great as a quick reference app—I find myself using it mostly on my iPhone to look up call numbers for sources when I’m at the library (I usually record call numbers in Bookends on my Mac for any sources that I plan on checking out later at the library).

      I did try to use the PDF reader built into Bookends on Tap when I first started experimenting with my workflow, but it just didn’t suit me. Another possible option for those who have larger (32, 64, or 128 GB) iPads is syncing all attachments to the Bookends app and then using the “Open in” function to open attachments in PDF Expert 5 for reading and annotation. This then requires you to use the “Open in” function again when you’re finished reading/annotating the PDF in PDF Expert 5 to open and update the PDF back in Bookends on Tap (see http://www.sonnysoftware.com/bookendsontap/styled-2/ for more detail).

      From my experience, using Bookends on Mac, Dropbox, and PDF Expert 5 on iPad has offered the smoothest and most feature rich workflow for what I need. Your needs might be different, though, so I definitely wouldn’t discount Bookends on Tap.

      Hope this helps.

      Reply
  3. Jeremie

    Great read, well written and nicely illustrated by screenshots.

    I have a few questions you might be able to answer from personal experience: What is your workflow when reading printouts of PDFs? Do you annotate them on paper and then recreate the annotations in the PDF? Or are printouts definitely passé and you do everything on the iPad?

    How do you handle summaries (that you’ve written) of your material? Do you just use a text or Word file and put it with the attachments?

    Reply
    1. Ben Lee Taylor

      Jeremie,

      Thank you for the compliments on the article.

      I have a few questions you might be able to answer from personal experience: What is your workflow when reading printouts of PDFs? Do you annotate them on paper and then recreate the annotations in the PDF? Or are printouts definitely passé and you do everything on the iPad?

      I rarely print PDFs, and not just for reasons of saving money and paper. Most of the PDFs I work with are OCR optimized, which makes it incredibly easy for me to search the text. Additionally, if I annotate PDFs digitally, I can also search my annotations and even print them out in a list format if need be.

      If you really can’t get away from reading printout PDFs, I would suggest using an app like TinyScan to scan the annotated text using the iPhone or iPad camera (I only have experience with iOS devices) once you’re finished with it. The great thing about TinyScan is that it can automatically upload scanned documents to your Dropbox account, although I’m not 100% sure whether or not you can specify where the files should go by default in your Dropbox account. If you could, in theory you could have them go right into a folder that is synced with PDF Expert 5 so that they’d automatically be there the next time you open the app on your iPad.

      How do you handle summaries (that you’ve written) of your material? Do you just use a text or Word file and put it with the attachments?

      This is a good question, but it’s one that I don’t have a good answer to. I have yet to integrate this kind of thing into my Bookends/PDF Expert/Dropbox workflow. I’ve become a huge user of Evernote over the past year, so that’s usually where summaries and longer notes/annotations end up going. I’ll then organize these notes based on author, subject matter, or overarching project.

      If I were to integrate this sort of thing into my workflow, I think I would do it by either 1) adding an extra blank page or two to the PDF I’m reading (which can be done in PDF Expert) and writing the summary on those pages directly on the iPad using the text tool in PDF Expert or 2) writing my summary/annotation on my Mac in a text document, giving this text document the same name as the PDF it is summarizing/annotating with the addition of a “- summary” appended to the end, and exporting this text document as a PDF to my Bookends folder in my Dropbox account. The latter solution appeals more to me because no matter how hard I try, I can’t seem to enjoy writing on an iPad (even with an external keyboard). However, there would be the downside of not being able to further edit the summary after exporting it as a PDF.

      Anyhow, I hope I answered your questions with as little confusion as possible, and thanks for reading my blog.

      Reply
  4. Luke Davoll

    Hi, just what wondering your workflow for when you want to export annotations using your mac. I’ve not found a way to do it using preview. What do you use? Great article by the way…

    Reply
    1. Ben Lee Taylor

      Luke,

      Thanks for the kind words. When you first left this comment, I didn’t have much of an answer besides, “I don’t generally export annotations from PDF documents using my Mac, or any other device for that matter, and a quick Google search didn’t really turn up much. Sorry.” Instead of giving that response, however, I thought I would return to the question when I had more time to do some research. Lo and behold, nearly two months later, I’ve come across a web application called Sumnotes that seems to be pretty good at extracting annotations from PDF files and exporting them into a relatively clean format. I gave it a go with a PDF in which I had done a bit of highlighting, and all of the highlighted passages were exported successfully (your document would have to be OCRed for this to work, of course).

      The basic service is free, but there are also two paid premium options. The biggest downside: Internet connection required.

      However, if you’re only using a Mac (which the wording of your question leads me to believe), your other best option might be to use Skim, which is a third-party PDF reader and annotation app. It’s free and open source, which is great, and it has an option to export PDF annotations as a text file. The only issue with Skim (and it’s a big one if your PDFs are getting tossed between multiple platforms or applications) is that it doesn’t seem to recognize annotations (text boxes, anchored comments, highlights, etc.) as “notes” when using the export “Notes as Text” feature. The image below shows the basic functionality of the feature, and if you squint hard enough, you might be able to see where I have chosen “Notes as Text” as the “File Format.” Skim Export Notes as Text Feature I tried it with two different files that I had annotated with either Preview on my Mac or PDF Expert 5 on my iPad, and the text files that Skim exported were both empty. That said, if you just work on your Mac, you could set Skim as the default PDF reader, and all PDF annotations you make within the app should export without any problem.

      I hope this helps, and if you’ve managed to come up with a different/better solution since you left your original comment, I’d love to hear about it.

      Reply
  5. Edwin K. Luk

    It took me quite a while to identify Documents / PDF Expert as the most suitable PDF reader to me on my iPad. I have been thinking how to get the dropbox, PDF Expert and Bookends work together. You saved my life. thannnnnnnnnks

    Reply
    1. Ben Lee Taylor

      Edwin,

      I don’t think I’ve ever saved anyone’s life before. You’re very welcome!

      If you’re interested in more of this sort of stuff, I’ll be publishing some new articles soon on how my workflow has changed in the past few months.

      Reply
  6. Kathy Love

    Hi, Ben, good to see you in cyberspace again! It’s great to see your PhD work getting on so well, and equally great to know you are still trying to help the rest of us work out how to use technology so that it becomes a friendly tool instead of a malign trap. I sent you an email a few weeks ago, reporting my progress with Excel and my initial experiences with Zotero (which seems to go much the same kind of thing as Bookends). Looking forward very much to your further articles on all this!
    All the best,
    Kathy

    Reply

Leave a Reply