Academic reference management: Some useful features in Bookends

Bookends, which I’ve written about previously here, has been my reference manager of choice for a while. In this post, I’ll highlight some useful features in Bookends that help me organise and manage my literature.

Keywords and smart groups

I’m a great fan of tagging in terms of organising my work, and I have a set of tags that follow me across applications on my mac. In Bookends, tags are called ‘keywords’, and I use keywords to organise all my literature. Whenever I import an article, I assign it relevant keywords based on the theme and the methodological and theoretical orientation of the article. I also make a note if it is part of a special issue, or if the empirical research relates to a particular country. An advantage with using keywords (and smart folders) instead of traditional folders is that you can assign an article to more than one category, which is key for how I work.

I then use these tags to organise my literature into smart groups. For example, I may create a smart group for all entries with the keyword ‘ethnography’. If I later add an article to Bookends and assign it the keyword ‘ethnography’, it will be automatically added to the ‘ethnography’ smart group. Smart groups are very flexible. While I mainly organise them by keyword, you can create smart groups based on a whole range of search combinations, including author, title, journal and text in the note cards.


Tag cloud

The key words you enter into Bookends are in turn organised into a tag cloud. In this screen shot, you’ll see the tag cloud for my whole reference library at the bottom.

Screen Shot 2014 01 04 at 22 19 22

You can tell Bookends to limit the number of tags shown to the top 50, 100, 200, 500, 1000, or alternatively, it can display all of them. I primarily use the tag cloud to view keywords, but you can also tell it to display authors and editors, or the most common words from abstracts or your notes.

In addition to offering a quick way to navigate your literature, the tag cloud can also be used to narrow down the number of articles in a search. For example, I might want to identify all articles with the tags ‘anthropology’ and ‘educational theory’. Using the command button as I click, I can select both of these tags, and the references containing both of these keywords will be displayed:

Screen Shot 2014 01 04 at 23 03 11

You can also ‘drill down’ the tag cloud itself. For example, I may start by selecting the tag ‘anthropology’, so that all references with that keyword will be displayed. Then, from the contextual menu in the reference set, you can select “Create Tag Cloud From This Reference Set” from the bottom of the list.

Screen Shot 2014 01 04 at 22 36 11

The tag cloud will then change to reflect only the references that contain the keyword ‘anthropology’:

Screen Shot 2014 01 04 at 22 37 55

…and from there you can narrow down further, based on whatever criteria you are working with. If you like tagging (which I really do), Bookends is a great tool to work with.


Each reference in Bookends has a hyperlink. You find the hyperlink by selecting a given reference and bringing up the contextual menu:

Screen Shot 2014 01 04 at 22 39 52

You can then use these links to connect the reference in Bookends to your literature notes kept elsewhere. For example, I keep a lot of my literature reviews in Circus Ponies Notebooks (which I’ve written about here and here). When I refer to a particular article in my reviews, I can just insert the hyperlink from Bookends. Then, if I’m reading through my notes in CPN and want to have a look at the original PDF in Bookends, I simply click on the link and it directs me straight to the relevant entry. This is what it looks like in CPN:

Screen Shot 2014 01 04 at 22 43 33


Integration with Devonthink

As I’ve written about here, Devonthink is a powerful data base that many academics use to organise literature notes. In Devonthink, there is a Bookends template for directly linking to entries in Bookends. You first need to select the relevant reference in Bookends. Then, switch to Devonthink, and find the Bookends template:

Screen Shot 2014 01 04 at 22 50 12

This opens a template which will automatically import the meta data for the selected PDF. It also inserts one of the hyperlinks described above, so that you can easily navigate to the original PDF in Bookends from your literature notes in Devonthink. The template looks like this, and from there you can add your own notes, import annotations, and so on:

Screen Shot 2014 01 04 at 22 52 16


Using labels

Bookends has labels that you can customise with the text and colour of your preference, and use to organise your literature. The label that I use the most is ‘in Evernote’. This indicates that this is a PDF that I have read and taken notes from, and that these notes are stored in Evernote. When you deal with a large number of PDFs, I find that it’s easy to loose track of what I have read, and what I haven’t. In this way, the entries I already have notes for are easily identifiable by a green label in my overview. Other labels include ‘to read’ for articles I should prioritise, ‘incomplete’ for entries that need editing or fixing, or labels that refer to particular writing projects.

Full text spotlight search

This was one of the main reasons why I switched from Sente to Bookends. Bookends offers a full text spotlight search of your entire library. Some of the things I use this for is to make smart groups of all texts that refer to a particular author, or which contain a particular concept. The spotlight search is available from the search field in the top right hand corner.

Tagging and searching note cards

Bookends is the only reference manager I know of with the capacity to tag individual notecards. The notes pane in Bookends, where you can insert any notes to an entry as you see fit, is divided into multiple notecards. These notecards can be tagged individually by inserting a % sign before the tag. For example, you could assign a tag to all notes that deal with a particular methodology, or a concept, and so on. These are in turn searchable. Bookends also gives you the general option to search notecards only.

So, these are some of the features in Bookends that I think are really helpful for organising literature. If you have other tips for how to use Bookends, please leave a comment below.

Related posts on this blog:

Managing your research literature: Sente versus Bookends

Reference Management: Exploring Sente

There’s another good blog post written by Ben Taylor on using Bookends in conjunction with PDF Expert here.

This entry was posted in literature review, note taking, reference management, workflows and tagged , , . Bookmark the permalink.

5 Responses to Academic reference management: Some useful features in Bookends

  1. benleetaylor says:

    Great post, and thanks for the mention! After reading this, I can tell that I still have yet to get around to using a lot of what Bookends has to offer (I’m particularly interested in labels and tagging notecards).

    Just to let you know, I plan on doing a follow up to my Bookends/PDF Expert post about taking advantage of PDF Expert’s two-way sync with Dropbox to eliminate the need to manually download/upload Bookends attachments when viewing them on the iPad.

    Looking forward to future posts 🙂

  2. tineschenck says:

    Hi, there.

    I just fell upon your blog, which is so useful for a fellow (Norwegian) Apple convert with all the bells and whistles. I am currently switching to Mellel which provides support for either Sente or Bookends, and after your reviews I am leaning towards Bookends. But, I thought I should ask whether you have any experience with Mellel and reference manager use (Mavericks)? As I just forked out for Mellel, I would like to know more before I purchase the software.

    Thanks for the blog, it is really a godsend to find other academics who are fighting the PC world in order to get read. 🙂

    • macademise says:

      Thanks for the comments, glad to hear that the blog is of use! I don’t have any experience with Mellel at all, but I’ve heard/read that it’s good tool and that it plays well with Bookends. I’m fairly sure both Sente and Bookends have trial versions (with some limitations to how many references you can use), so you could test them out for a bit before you spend any more money. Good luck finding a reference manager that suits you 🙂

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