Managing your research literature: Sente versus Bookends

While I have been using Sente for a while to manage my PDFs, I’ve been curious about Bookends since I first heard about it, and recently I decided to check it out. In this post, you’ll find my first impressions of Sente versus Bookends, with a focus on

- the mac versions (I’ll address the iPad versions separately in a future post)
- importing, organising and annotating references and PDFs

For those interested in cite while you write functionality, I’ll state up front that I won’t be addressing that here. I am still sticking to EndNote for formatting my research papers; in spite of its clunkiness and old fashioned streak, in my experience it’s the only app I can really count on to a) function on all the library and journal web sites I regularly visit, and b) import and format reference information with the highest level of accuracy. However, EndNote is not very useful for organising PDFs and also doesn’t come with annotation capacities; hence I use alternative apps for those purposes.

If you haven’t already read my first post on Sente, I encourage you do to that before continuing this post, as I’ll be referring back to it here. Since that post contains quite a few Sente screen shots, I’ll also be using more space here on displaying Bookends (with a bit of empty space after a few of the screen shots which for some reason I can’t mange to format away…)


User interface

In several ways, the UIs of Bookends and Sente are quite similar. Both offer list and standard views, with a tool bar on the top, a library view to the left that provides an overview of folders, smart groups and other organisational features, a reference view to the right that offers different windows where you can view additional information about the selected reference or edit reference information, and a third pane below where you can view the attached PDF or related web sites. In Bookends, you can also use the lower pane to see the tag cloud, which I’ll talk more about below.

Here are some screen shots for comparison, with Sente first and Bookends second.






In Sente, you can easily rearrange your library according to title, name of authors, dates added or modified, and a range of other criteria. Bookends offer similar options, but it’s more cumbersome if you’re not in list view, because you need to select all references, right click, navigate to ‘sort by…’, and then select your option. If you are in list view, however, you just set up the columns according to your preferences, and then you can easily rearrange your library based on e.g. author, title or date added.

In the left library pane, Sente also offers the option of filtering your references based on different time frames of recent modifications, as well as by rating or status.  The library pane of Bookends, on the other hand, offers quick navigation to terms lists of authors, journals or keywords, plus default smart groups of authors, recent searches, and attachments. In Sente, the term lists are accessed via an icon in the upper tool bar.

Importing references and attaching PDF files 

Both apps have a variety of options for importing references and adding PDFs, including

- a built in browser
- drag and drop PDFs
- if you have a PDF file open in Safari, use the ‘print to Bookends/Sente…’ function in the print menu

I find the built in browser of Sente more user friendly than Bookends’. Its targeted browsing (see previous post) makes importing references very smooth, and when I click on ‘open pdf’ on a journal web site, the related pdf file will immediately attach itself to your latest added reference (you can also choose to attach it to an already existing reference or a new reference). In Bookends, attaching the pdf acquires an additional step – a minor difference, though, to be fair.

I find importing references through Bookends’ browser a bit more cumbersome. First, when you import references into Sente, you can edit the reference information and add tags. In Bookends, this has to be done after you have completed the import, so adding tags/keywords is more time consuming in Bookends than in Sente and becomes a separate operation. Also, when you search google scholar in Bookends, the app has added an additional ‘layer’ between you and the web site for importing reference information, whereas Sente allows you to more directly navigate the actual web page. In sum, it’s not that Bookends is bad, it’s just that Sente is smoother. Below you will see a screen shot of Bookends’ in built browser. The green dot in the top right hand corner mediates import of your reference information, while the quadrangle is the tool for importing PDFs.

Bookends browser

With regard to drag and drop, however, Bookends offers an advantage in that you can just drag and drop a pdf file from the finder window down to the Bookends icon in the dock. This is a very useful feature that Sente doesn’t provide – you can, however, drag and drop a file on to the library section of its UI, but if this isn’t visible at the moment you’re dealing with the Finder, it adds a few more steps to the process. When using drag and drop, Sente will automatically open a new reference pane and will first conduct an automatic search for the reference information. If the search is unsuccessful, you can edit the information manually. If it finds a reference already containing that PDF, it will offer you the option of updating the existing reference.  When you drag and drop to Bookends, it will offer you the choice of attaching the PDF to the currently selected reference, or creating a new one.

In both apps, you can drag a PDF file directly on top of a selected reference, and the PDF will then be attached. While I haven’t tested it extensively, the ‘print to…’ feature in Safari also seems to be working fine in both apps.

Between the two, Bookends excels in dealing with duplicates. One downside to Sente is that it doesn’t have a manual way of searching for duplicates. Although it claims to identity duplicates upon import, my experience is that it has missed quite a lot of doubles. Bookends comes with a manual search for duplicates, and you can chose whether you want Bookends to just delete the duplicates, or inspect them first and then delete manually.

Overall, I find Sente smoother for importing references from the web, while Bookends is more convenient in that you can drop PDFs directly on its icon in the dock, and also makes it easier to deal with duplicates.

Options for organising your PDFs

In both Sente and Bookends, you will be offered static groups and smart groups (called ‘groups’ in Bookends and ‘collections’ in Sente), and Bookends also adds another level of organisation with folders. A smart little feature in Bookends is that when you hold down shift and option keys when a reference is selected, the groups that the reference belongs to will be highlighted in yellow.

In addition, Sente offers brilliant options for hierarchical tagging (see my previous post), which is probably my favourite way of organising literature. Working with tags in Sente is very intuitive and flexible.

Bookends, on the other hand, has a nice tag cloud. The tag cloud aggregates all kind of information – I primarily use it for keywords, which is what you see in the screen shot below. Instead of keywords, you can adjust the tag cloud to display names of authors and editors, or words from titles, abstracts or notes. In the preferences, you can ask Bookends to ignore particular words to refine your tag cloud views, and you can also specify how many tags you want Bookends to display in a tag cloud view (top 50, top 100, 200, 500, 1000 or all of them).

Bookends tag cloud

Personally, I prefer tagging as a main organising principle in Sente, and smart groups in Bookends which are in turn grouped in folders. The tag cloud in Bookends provides an additional way of navigating and exploring my reference collection, but although I find it a really cool feature, I don’t rely on it as a main tool for organisation. More generally, both apps offer rich options for organising your literature – your choice might come down to personal preferences, such as wanting the hierarchical tagging offered by Sente, or the tag cloud offered by Bookends.

Annotation capacities

In terms of annotation capacities, Sente has the comparative advantage in the mac version, offering three main options for annotation: highlighting in different colours, adding notes, and a quote function. Bookends has notes, but otherwise doesn’t have annotation features in the mac app (it does, however, in its iPad version). From the Bookends user forum it seems that a lot of people are marking up their PDFs using Skim, and then sending the PDF back to Bookends.

Sente’s quote feature, which I wrote about in my previous post, is very useful – basically, it copies the text you highlight in the pdf and then allows you to attach your own notes directly to the exported text. A somewhat similar feature in Bookends is to highlight text in the PDF and drag it to the notecard of the reference, but the app won’t automatically distinguish the quote text from ‘regular’ text, and it also won’t reformat the text so you can end up with some odd line breaks.

If you download an Apple script from the Sente web site, you will be able to export your notes from Sente, a feature I use to transfer notes from Sente to Circus Ponies Notebooks, which I use as my hub for literature review notes. This is a very useful feature, although some of the formatting gets lots in the process. I haven’t found a script for doing anything similar with Bookends. It does have a ‘copy notes’ feature, but when I’ve used it the text in the notes haven’t been separated when I’ve pasted them, which means spending time on clearing them up.

Having said all that, I do 99% of my reading and pdf annotation on my iPad, so I’ll be addressing annotation capacities more in detail when I review the iPad versions of both apps in a future post.

Searching your PDFs 

This is one of the biggest let downs of Sente; currently it doesn’t offer full text search within a single attachment, or of your full pdf collection. I was pretty amazed to find this out, given that this is a really basic task when you conduct research. The developers have promised full text search of single documents in their next update, but say that full text searches of entire libraries are not part of their future plans.

Bookends, on the other hand, offers spotlight searches of your entire library. I find this feature extremely useful – for example, I might want to review all my PDFs containing the words ‘knowledge mediation’ or ‘Vygotsky’, and Bookends allows me to create smart groups for such literature searches. This feature was one of my main motivations for considering Bookends as an alternative to Sente.

In terms of conducting other kinds of searches within your collections, both apps let you search by a range of criteria such as author, title, year, keyword or ‘anywhere’ in the reference. Sente has a smart filtering feature where you can narrow your search step by step. For example, you can start by identifying an author, then filter her publications by year, then by tag and publisher, and so on – see screen shot below for illustration:

Sente filtering

While I think Bookends actually facilitates something similar through the option of ‘pinning’ entries in the term list, I haven’t managed to figure out how to do it yet. Bookends, on the other hand, has more search criteria than Sente when doing a one level search. It also has the very helpful feature of allowing different term list entries to be merged. This is extremely useful when you have three or four entries for the same author that only differ in punctuation or in whether the first name is spelled out. In Bookends, these four entries can be merged into one, in Sente they cannot.

Syncing to your iPad

In this area, nothing beats Sente, with its automatic sync between mac and iPad. Basically, you don’t need to think about it – it just happens. While I’ve had incidents where the sync is delayed and they occasionally have issues with their sync server, this feature is generally extremely useful. Personally, I rate stuff that ‘just syncs by itself’ very highly – if you need to manually sync ten different apps between your mac and your iPad, it starts taking up significant time and effort, and you typically forget to do it exactly when it’s needed.

Bookends requires a manual sync where your mac and your iPad are on the same network (or alternatively, you create your own network between your mac and your iPad, see a how to guide towards the end of this page). Once you’ve set it up it’s relatively straight forward, although I’ve experienced issues when on large institutional networks and I’ve then had to set up a separate network between my mac and my iPad. Even then, I’ve had some difficulties and although I don’t think my experience with this is particularly representative, it’s generally difficult to beat Sente’s set up where the sync just takes care of itself.

Concluding comments  

One area where Bookends beats Sente is that of support – developers are extremely responsive and follow up multi step queries; my personal experience is that support at Sente is a bit more sketchy. On the other hand, the user guide of Sente is generally better written and a bit more pedagogical – however, both apps come with extensive and detailed user manuals.

So, which one should you chose? Both options are high quality reference managers that offer a multitude of features for organising your research library. I have only scratched the surface in this post, so make sure to consult the respective user forums and manuals before you decide what to buy. Here are some criteria to consider:

- if you like organising your literature by tags, Sente is the way to go, while Bookends will push you towards smart or static groups, complemented by their tag cloud
- if you want to be able to do full text searches of multiple attachments, the obvious choice is Bookends
- if you don’t want to have to think about syncing to your iPad, go with Sente

My top three features in Sente: the mac/iPad sync, the tagging system, and the built in browser
My top three features in Bookends: full text searches that can be converted into smart groups, iAnnotate integration on iPad, and outstanding support

If you have an iPad, you should look into the details of the iOS apps before deciding which reference manager to go for – I’ll be covering them in a future post on this blog.

You might also want to consider Papers, another high quality app for reference management that also comes with a Windows version, which makes it very interesting if you work in a Windows environment but have a mac at home – have a look at this comprehensive review of Papers versus Sente on AcademiPad here and here.

Related posts: Reference Management: Exploring Sente

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About macademise

I am a researcher working in the intersection of anthropology, learning and cognition.
This entry was posted in literature review, pdf annotation, reference management and tagged , . Bookmark the permalink.

15 Responses to Managing your research literature: Sente versus Bookends

  1. Dellu says:

    I think the most important feature of Sente for the academicians is the Annotation feature. In my view, the annotation feature is the one that puts Sente ahead of all other PDF readers and bibliography managers (Adobe, Skim, Docear, Mendeley, Jabref, Papers, Bibdesk, Bookends, Zotero, you name it, I have tried them all by the way; Jabref and Bibdesk for Latex; Mendeley is great in many areas, docear is promising). There is no any app, both in the windows and mac, that can elegantly do PDF annotations as Sente does. That is the single most impotant reason I bought the app. Skim is great for annotation in mac (Foxit or PDFxchange in Windows), but the fact that you don’t have a clear way of distinguishing quotations from your own notes (comments) can put you in trouble in the long run…plagiarism. Plagiarism is the main reason I decide to avoid Skim. In Skim, you quote the article, and put your comments in the same place (notes window). Some day, you can forget which sentences are yours and which are the author’s. Sente handles these things perfectly; you have your own place to put your comments, and a separate place to quote the article…safe and clean.
    Great article by the way!

  2. I’m looking for a way to enter block quotes from print books as well as from ebooks or PDF documents. I’d then like to be able to tag these quotations into various categories so I can use them in future writing and teaching projects. Will either of the two products that you reveiwed be able to accommodate this, or can you recommend a solution that would?

    • macademise says:

      Sente has a very good option for converting chunks of text from pdfs into notes, but it only allows tagging at reference level, not note level. Bookends let you tag your notecards, but you would have to open the document in Skim/Adobe reader/any other pdf viewer to actually cut and paste the text. Here’s what their user manual says about tagging:

      You can enter tags (keywords) to your notecards that can describe the contents of the notecard and be found by searching. A tag must be preceded by a % (percent symbol), and all tags must appear on a single line, before or after the note.

      If you look at my post on Scrivener, which is here, I have quoted someone else’s literature review workflow, and it sounds like what you are looking to do is very similar. This also allows for conveniently putting your quotes and your text-in-progress side by side when you start writing.

      Another option to look into is DevonThink. I haven’t reviewed it, but you can look at their web site here. This is an extremely powerful app, which allows you to either import or index your research library, and then you can create notes that are related to these, and everything can be tagged. Don’t be put off by the slight learning curve of the app, it takes a bit of time getting used to but has a lot of rich features.

      Yet another option is Circus Ponies Notebooks, which I’ve written several posts about – click their name in the tag cloud on my home page. They are, as far as I know, the only note taking app (as opposed to reference apps) that allows tagging of selected pieces of text on a page (as opposed to pages/ whole notes). You have to use outline mode to do this.

      I don’t know if you’ve used Evernote? EN also has a very convenient tagging structure where you can apply multiple categories to a note, but you apply the tags to the whole note rather than selected pieces of text within it. If you’d be happy to create a separate note for each quote, then that could also work.

  3. Dellu says:

    I have also been searching for a tool that can tag a specific note (bullet point). Ponies Notebook can assign keywords to specific bullet points. But, the problem with Notebook is, these keywords won’t be exported; the keywords are locked down into the app.
    One strategy I am using right now is to mark may keywords with special markers as [[Keyword]] wherever I write my note (inside Sente for example). Then, I use searching tools to pick those words inside the [[]]. Theoretically, this can be achieved in every app; and can be converted to any other kind of tag (openmeta). But, in practice, very few apps can search special symbols. Hence, I use Tinderbox to this purpose; assign Agents to collect those [[Keywords]] and convert them from in text notes to actual tags.

    • macademise says:

      Thanks for that – I have never tried Tinderbox but it looks really powerful. What space does it occupy in your work flow?

      As I said above, Bookends allows for tagging note cards (the only app I know which does this apart from CPN), but I don’t know of any way of exporting them with tags intact.

    • Paul says:

      @Dellu: How do you collect the hardcoded keywords in Sente 6 with Tinderbox?

  4. versaceyoyo says:

    This was a great post. I am at a crossroads with Sente. I have just produced a 20,000 word manuscript using Sente for the lot-my reading, marking up pdfs, inline and reference list generation. However, given I will need to produce an 80,000 word manuscript next year, I simply cannot face the stress that Sente has caused me again on this smaller project. It is just so unreliable in its scanning and generation of the references in the manuscript. Is Endnote really more reliable than Sente? I am seriously considering exporting my library to Endnote and using it in future, but sticking with Sente for reading and annotating. Would love your thoughts (esp on how Endnote goes in Pages)…

    • macademise says:

      Thanks for your comment. Personally, I have stuck with Endnote for referencing my academic papers. While it’s not ideal to work with two apps instead of one, both Sente and Bookends are just much better alternatives for pdf management, especially as Endnote was extremely late to the game with an iPad app, which then didn’t get very good reviews. However, in terms of importing references into the database and referencing my academic papers, I find Endnote to be much more accurate. Because I’ve used it for about fifteen years, I’m also more familiar with it when it comes to modifying styles and so on. So, I work with Bookends and Endnote in tandem. I hope, at one point in the future, that I’ll be able to switch permanently to Bookends. I might try to do a shorter academic paper with Bookends a bit further down the road.

  5. benleetaylor says:

    I just started an M.A. program this past fall, and, after much research, I chose Bookends as my reference management app. It’s worked out great for me so far, especially alongside PDF Expert on my iPad. If anyone is still considering Bookends as a reference manager and would like to know more about how I’ve been using it, I wrote up a little something today about my workflow with Bookends, PDF Expert, and Dropbox. You can read it here:

    I just thought I’d revisit this post, as it was something that helped me decide on Bookends in the first place :)

    • macademise says:

      That’s a great blog post, Ben, I’m going to link that up on my latest Bookends post as well (which is here).

      • benleetaylor says:

        Thanks! I hadn’t seen your latest post on Bookends. I just popped it into my Read Later list—I’m trying to get more sophisticated with using some of the advanced features Bookends has to offer, so I’m sure this will be a helpful post to check out.

        Take care.

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