Bookends: The Most Link-Friendly, Interoperable Reference Management Software on Earth

I’m not only CEO of CogSci Apps Corp. I am also an adjunct professor of Cognitive Science and of Education at Simon Fraser University. I write academic papers and books. As such, I rely heavily on reference management software. When Readcube transitioned from Papers3 to Papers 2020, I realized I had to ditch the Papers app. Readcube dropped AppleScript support, pushed the concept of storing PDFs on their website, and moved towards a subscription service. I value interoperability (which AppleScript provides). And I’m unwilling to store my precious PDFs in a foreign company’s cloud service. (iCloud syncing is in a different, very acceptable, category.)

After studying the options and consulting with my peers, Bookends was my clear choice. Why Bookends rather than, say, Zotero? In the end, it was simple. Like Hookmark, Bookends is made for the Apple platform; it has excellent automation; it syncs via iCloud while offering an alternative; and it is highly recommended by many Hookmark users 😊.

I am delighted to report that I have been very impressed by Bookends. One of the papers I’m working on has over 250 references. Bookends handles it exceptionally well!

Bookends is very link-friendly

One thing I particularly love about Bookends is that its developer really understands the importance of link-friendliness. Bookends has long been link-friendly. But in the last six months Bookends has added a lot of additional support for linking, including link automation.

This means that Bookends is far ahead of the pack of reference management apps on any platform (not just macOS).

So it is with great delight that I announce that

Bookends in Hookmark’s Partner of the Month of April 2023

The Bookends developer, Jon Ashwell, and I have been communicating ever since I first considered switching to Bookends. I’ve been consistently impressed by his software, dedication and understanding of the importance of interoperability and linking.

So, it is a tremendous honor, pleasure and privilege to partner with Bookends!

Taking notes about PDFs

Over the last 20+ years of R&D on cognitive productivity, I’ve consistently noted that as useful as in-line PDF annotations can be, it is important to be able to take detailed notes about PDFs in multiple special-purpose apps of one’s choice. I don’t just mean traditional “note-taking” apps. Any information can be a note with respect to any other information, as long as it’s in link-friendly software. In order to do this, the PDF software and the “note-taking” software needs to be link friendly.. Bookends is link-friendly, as are many many “note-taking” apps for the Mac. That means that one can connect Bookends’ PDFs to information in other link-friendly apps.

I’ll cut to the chase by showing and discussing a couple of screenshots of using Hookmark with Bookends.

The screenshot below shows Hookmark, invoked in Bookends on a paper I’ve selected and to which I previously hooked a lot of information.


You can see that I previously hooked that reference (Beaudoin, Luc P. 2020) to

  1. an OmniFocus reading plan,
  2. an email from a co-author,
  3. an Apple note,
  4. another PDF in Bookends,
  5. A Figure (“foo bar baz”)
  6. a folder on Finder
  7. a mind-map (about the paper),
  8. an outline about the paper, and
  9. The Word version of this paper (given that I am its lead author).

This means I can quickly, bidirectionally, navigate between the “notes” and the PDF. I don’t typically connect so much information to any particular PDF. But when I a PDF is very important, I do typically hook it to one or more of the types of information listed above.

Connecting a PDF to a paper I am writing is a particularly interesting use-case, which I discuss next.

Writing papers with Hookmark and Bookends

The screenshot below illustrates how handy it is to use Bookends and Hookmark together when writing a long paper. In this case, I’ve created one folder on Finder for each section of the paper I’m writing. Notice that in Section 11 of the Word document, I pasted a hook://file/ link directly in the Word document. That way I can click on the link to get straight to the folder containing information pertaining to Section 11. The hyperlink will be formatted as hidden text before it’s sent to the editor 😉.

I’ve also hooked the following type of information to the draft, so that I can quickly navigate from the draft to it:


  1. The OmniFocus project containing my TODO list for this paper.
  2. A link to the shared Dropbox folder containing an output, revision history, feedback from co-authors, etc..
  3. The Grammarly page this paper in which I check one part of the paper at a time.
  4. A bunch of PDFs. Most are bookends:// links; but a couple are hook://file/ which open in Skim (the call for papers and an infographic).
  5. an outline of my paper (in OmniOutliner).

Of course, you can use other apps than the ones listed above. Instead of

  • Finder you could use Path Finder, DEVONthink, etc.,
  • OmniFocus you could use Things, TaskPaper;
  • Dropbox, you could use Sync, Resilio etc.; and
  • OmniOutliner, you could use Bike or other outlining apps.

The concept is the same, so long as you’re using link-friendly apps.

If your favorite software is not link-friendly, sign the Manifesto for Ubiquitous Linking and email your app developer to let them know you don’t want your info stuck in a walled garden. We have found that many Mac developers can make their software link-friendly in half a day…

Deep PDF links

If you want to capture deep links to PDFs in Bookends, you can use the Bookends interface directly:

  1. select text in the PDF;
  2. control click; and
  3. choose Copy Link from its popup window

Alternatively, in Step 2 you can simply use Hookmark’s Copy Link command (or one of its variants) directly. Hookmark will automatically give you a deep PDF link. An advantage of using Hookmark’s Copy Link is that it is habitual. You can use Hookmark’s Copy Link in any link-friendly PDF app.

Here is a deep PDF link:


You can paste deep PDF links in your notes, tasks, or elsewhere. When you click on a deep PDF link, Bookends will take you to the precise page and the location on that page from which the PDF link was copied.

I’ve mentioned this functionality previously. However, we are receiving so much praise from our customers about Hookmark’s deep PDF linking being a “game changer”, I want to make sure everyone who relies on PDFs knows about this feature.

For more information about Bookends and Hookmark

There’s more information about Using Hookmark with Bookends Reference Manager by Sonny Software on our website. We’ve updated that page to reflect new linking functionality in Bookends app. The page will soon contain a screencast about using Hookmark with Bookends.

Check out Bookends on its website.