Super-charge your PDF workflow with Sente for Mac

Finding, reading, annotating, and citing journal articles is our daily bread as academics. But are we good at cutting it? How many times have you searched for “that perfect paper” you have read just a few weeks ago!? Or have you ever almost missed a submission deadline because compiling the bibliography “took a little longer”?

If you are reading a lot of journal articles (and chances are you do if you are in university), it makes sense to invest in a tightly integrated ecosystem that allows you to organize and annotate your PDFs seamlessly on the Mac and the iPad. As I mentioned in the previous guide to annotating PDFs, there are right now two contenders in a neck-to-neck race of offering the best, multi-device PDF management system: Sente and Papers. To keep the current review of Sente for Mac somehow manageable (Sente’s user manual stretches over 316 pages, just to give you an idea), it only covers the most basic functions: how to add a PDF (or reference more generally), how to organize your references, what annotations are supported, and how you can insert in-text citations and bibliographies into your write-ups.


Overview of the Sente ecosystem

First, however, let me describe briefly the Sente ecosystem. Sente is available for the Mac ($90 for a full academic license, $35 for a limited undergraduate edition) and for the iPad (now free for small libraries, but power users will need a subscription starting at $20 a year). You can sync your database between your devices through the Sente cloud, so your iPad does not have to be on the same wireless network as your Mac. In fact, you can synchronize your library across any number of Macs and iPads around the world (including all annotations, tags, and customizations), which is a great benefit if you are working with (Mac- or iPad-using) co-authors.

If you are rocking both a Mac and an iPad, it makes most sense to have both apps and to use the Mac app as the main tool for adding, organizing, annotating, and citing your PDFs, and the iPad app to read, annotate, and tag your PDFs on the go. This way you make most the use of the better multi-tasking features of your Mac, while at the same time you have the convenience to read your PDFs on the couch with your iPad.


The main window: Less eye candy, more power bar

Sente’s main window is a little cluttered on the first view and not as minimalistic or playful as you are used to from other Mac apps (e.g., Papers), but don’t let this deter you from testing out this app. The library tab displays your collections (sorted in various ways), the content of the active collection, the attachment, and an info plane that can show your notes, tags, and a preview of how this paper would be cited.

In order to read a paper, you can open it in a tab. Unfortunately, it is not possible to re-arrange the tabs or to open tabs in their own window. Because of the latter, you are only able to view one PDF at a time, which is a major grievance for me, as I would prefer to open two or three PDFs next to each other and read them side-by-side.

Here is a look on Sente’s main window (click to read short version of this post):

Sente's user interface is a little cluttered, but very rich on information once you got used to it. One of the biggest strengths of Sente is its focus on tagging as a way to organize your library. However, this is also one of the main reasons why Sente has a steeper learning curve than you would hope for.

Sente’s user interface is a little cluttered, but full with useful information once you got used to it. One of the biggest strengths of Sente is its focus on tagging as a way to organize your library. However, this is also one of the main reasons why Sente has a steeper learning curve than other apps.

In the screenshot above you also notice a floating QuickTags box. I have this one open all the time, as assigning tags is the preferred method in Sente to organize your library (see below).

The full screen mode in lion is simply the same window taking up the whole screen. In my opinion, Sente could have done better here by offering a dedicated reading view that gets rid of the toolbar and simplifies the user interface (e.g., better integrating the quick tags box).


Adding references to your database

Adding reference in Sente is pure joy, as most PDFs these days will be automatically identified when you are adding them to your database. In fact, the ease of organizing your PDFs is one of the main reasons for adopting a PDF management system (Sente or Papers, both are great), as all relevant data such as authors, journal, and publication year will be added to your PDF without much effort on your side. Sente can handle an impressive list of reference types (including Journal Article, Book, Book Chapter, Newspaper Article, and Webpage), and you can always add your own custom reference type.

PDF Management Systems make your life easier by matching your references with online databases.

My favourite way to add a reference is to simply drag a PDF I already have on my computer into Sente (unfortunately, it is not possible to just drag it on the icon in the dock). In most cases,especially if it is a recent publication from a major journal, the article will be identified immediately on its own.

Sometimes Sente is unable to find a matching paper automatically (this would be because the PDF file does not have a digital object identifier, or DOI, assigned). In this case, you can copy the title of the article and let Sente search for it online (e.g., using google scholar). You can also add references to your database by hooking up Sente with your university library or by using research databases such as Web of Knowledge.

Whatever way you prefer, the bottom line is that in most cases adding references to your library is a matter of seconds. In the rare cases that Sente cannot find a match to your paper (maybe it is not published yet), you can always add information by hand. Check out the picture gallery at the bottom of this post to see Sente in action.


Sente wants you to organizing your PDFs using tags

While the ease of matching references to a database sets PDF management systems (like Sente and Papers) apart from other apps for reading and annotating PDFs, Sente and Papers take slightly different approaches to the organization of your database. Separate posts on Paper’s approach and a showdown between Sente and Paper will follow soon on academiPad, so be sure to follow me on twitter for updates.

The idea of PDF management systems is that you can have one and the same paper in more than one collection. That is different to other apps, such as iAnnotate or PDF Expert, that let you organize your files in a folder structure. In a folder structure, you have to make copies (or at least a shortcut or alias) of a file if you would like to associate the same article with different projects. In a PDF management system, you always only have one file, but you associate it with as many different collections as you like. For example, you could have one collection for each of your ongoing research projects, or you could associate a journal article to different collections based on the theories that are used and the context the research is situated in.

Tagging explained for five-year-olds: If you wanted to associate this pen with the projects “pen”, “sharpie”, “marker”, and “purple” in a traditional file structure, you would need four pens (or at least one pen and three aliases) for this. Tagging allows you to have only one pen, which can be associated with as many projects (e.g., “drawing”, “buy more of these”, “smells funny”) as you wish.

Sente comes with a couple of useful standard collections to find recently added or manipulated papers and to sort your library according to the status (e.g., To Be Read, Done, To Be Reviewed), type, QuickTag, and your rating of a paper. You can also create manual collections into which you can drag references; however, you won’t be able to sync these manual collections with your iPad or other Macs, so I would use manual collections as little as possible!

Instead of manual collections, Sente wants you to organize your database through tags. This emphasis on tagging is both one of the biggest advantages of Sente, but it is also one of the main reasons why Sente has a steeper learning curve than its competitors. I will write more about the awesomeness of tagging sometimes later, so let’s get back to how you can organize your Sente library in the most efficient way.

You can also add tags while reading through the article in the reading tab, either by using the QuickTabs box or by just writing a new tag in the notes plane.

You can add tags to your references during the import, from the main library window, or when reading the article in its own tab. Besides adding tags by writing them into the tags field, you can also add your most important tags to the QuickTags box. This is a great way to organize your database, because you can nest your QuickTags into a hierarchy of tags.

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Let me repeat, because this is the key for understanding Sente: You can organize your QuickTags into a hierarchy. So instead of creating a hierarchy of manual collections (which was my first instinct when I tried out Sente), you create the hierarchy for the tags! This way, all you have to do is to assign tags to the article and it will show up automatically in the By QuickTag collection that grows every time you are adding another tag to the QuickTags box.

In addition to the QuickTags collection, you can also create customized smart collections that can also be put into a hierarchy. This might be especially important if you want to have a collection that is about a specific, important theory (I would have a QuickTag for this) and that is published in a particular journal or that has a rating of higher than three stars. Both your QuickTags collection and your customized smart collections can be synced.

Besides tags, you can also navigate through your database using hotwords and the browsing mode. The latter is kind of an ad-hoc smart collection and I don’t use it very often. What is nice though is the hotwords function, which highlights specific words in the titles of the references. The good new is that you can freely customize your hotwords, but the bad news is that the hotwords function works right now only for the reference metadata. That means that it won’t highlight an article that uses the hotword in every second sentence but not in its title.


Sente has the best workflow for annotating PDFs on your Mac (no, really!)

Sente for Mac has a killer workflow for annotating your PDFs. You simply select the amount of text you want to highlight, and an annotation toolbox will appear above the text. In this toolbox, you can select one of six colours (not customizable) and whether you want to highlight, comment, or quote the passage. Sente will remember the last colour you have used, but even if you are frequently switching between colours as I do, Sente makes highlighting really easy and fast.

But the annotation magic does not end here. If you choose either Comment or Quote, the passage will not only be highlighted but Sente will also add a colour-coded sticky-note in the Notes section where you can write down your own ideas (and the original passage of the article, if you opted for Quote). What is great about this function is that all your notes are in one place, so you can get a good idea what this article is about by simply glancing through your notes and comments.


In-text citations and end-text bibliographies

The other beautiful thing about PDF management system is that they make your life a whole lot easier when it come to citing others’ work in your writing. Sente works with pretty much every word processor you can think of (Pages, Microsoft Word 2008 and 2011, Mellel, Scrivenger, Nisus Writer, Open Office, and everything in between that uses the RTF format).

You can either jump back to Sente and add a reference thought the toolbar icon or via the Command+Y shortcut, but you can also just cite from within your word processor by putting you the reference you have in mind into a delimiters (e.g., [Scholz 2011]). I prefer using the latter method, as it doesn’t require me to interrupt my writing flow. Also, I changed the default setting of the delimeter from {} to [] because it is easier to type (however, I had to use {} in the example below because of html coding, oh well…).

Sente works with pretty much every word processor you can think of. To not interrupt your flow, I recommend to use placeholders such as {Scholz 2011} without leaving the word processor. I also recommend to cite Scholz as often as you can.

Sente works with pretty much every word processor you can think of. To not interrupt your flow, I recommend to use placeholders such as {Scholz 2011} without leaving the word processor. I also recommend to cite Scholz as often as you can.

Once you have finished your document, just add a [bibliography] tag to the end of your document and tell Sente to scan it. Like magic, Sente will replace all your reference shortcuts with the proper citations and add a reference list. Sente will be smart to follow citation guidelines (e.g., changing from “Scholz, Smith, and Mitchell 2013″ to “Scholz et al. 2013″ after the first citation), and you can select what citation style you want to apply from an impressively long list of built-in formats (you can also modify/create your own style in the Bibliography Formats editor).

But hey, what if I have special needs when citing papers, such as adding page numbers (“Scholz 2011, p. 397″) or when I only cite the year (“As mentioned by Scholz (2011)”)? No worries, Sente has you covered! You can add modifiers (e.g., Scholz 2011@397, %Scholz 2011) to your citations, and Sente will adapt the way in which it displays the citation. You can find out more about these modifiers in the Sente manual under “Modifying In-Text Citations” (p. 261).


Wrapping up: customizations and shortcomings

If you have made it this far in reading this post (congrats!), you might have gotten the impression that Sente is a powerful app that helps you in all aspects of your search-read-cite academic workflow. And damn right you are! Sente leaves behind other PDF annotating apps (e.g., iAnnotate, PDF Expert) in its rear mirror, and compared to its closest competitor, Papers, it puts up a great show. Especially with its focus on tagging and its killer annotation workflow (for the Mac, but not so much yet for the iPad – see future post), Sente makes a great pitch why it should be your future PDF management system. Also, many features of Sente are fully customizable. For example, you can add or edit QuickTags, status, hotwords, reference types, and bookmarks.

However, Sente also has a couple of problems. First and foremost, I find that Sente has a steeper learning curve than other apps. This is mainly due to its focus on tags (but once you got the idea of tagging, you never want to go back), and also Sente’s interface is not as clean as it could be (it was recently re-designed, and the annotation toolbox is definitely a step into the right direction!). Also, I find it disappointing that there is no way to read references in their own Sente window (not in a tab), for example to read two articles side-by-side. Right now, you can’t even re-order the reading tabs!

Unfortunately, Sente does not allow to open references in their own window to read them side-by-side. Standard PDF viewers such as Skim let you do this, and it is a great way to justify to yourself buying that larger screen you really only need to watch movies on. I hope a window view will be added to Sente sometimes in the future.

Unfortunately, Sente does not allow to open references in their own window to read them side-by-side. Standard PDF viewers such as Skim let you do this, and it is a great way to justify to yourself buying that larger screen you really only need to watch movies on. I hope a window view will be added to Sente sometimes in the future.

Then there are other things that hopefully will be fixed in the near future. Right now, it is not possible to search for text within the PDFs. This is pretty bad, and I am sure that the folks at Sente are working on this as we speak. In addition, I would like to be able to add some overall notes to a paper (right now, I am using a “summary comment” on the first page) and to customize the colours for highlighting.

Overall, I think that these shortcomings (minus the missing text search) are very minor. Sente for Mac, since its version 6.5 release, is a very solid application for managing and organizing your PDFs (and books) that will grow on you over time.

But before you browse to Sente’s online store with your credit card in-hand, check out Sente’s iPad companion app as well as what its closest competitor, Papers for Mac and Papers for iPad, has to offer. Please subscribe to my twitter account to be notified when anything new happens with Sente or Papers:

Here are a couple of more screenshots showing you how to add references to your library and how the annotation workflow looks like:

Disclaimer: The developer of Sente granted me a review license for Sente for Mac upon request. Tagged sharpie image by, Sente on MacBook Air and the Word Processors images by Sente. All other images by academiPad. Please consider sharing this article if you found it useful.

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  3. Kate says:

    Really useful article – wish I’d discovered these options for pdf management earlier!

    I’ve trialled Sente for Mac and there was one issue that put me off the app – I wondered if you knew a fix or whether this is just a downside of the program itself or the pdf format. Within my discipline, footnoting (as opposed to in-text citations that seem to dominate the examples above) is more or less the universal referencing system. When attempting to highlight across pages, the Sente highlighter includes the footnotes in the quote/highlighted area before continuing on with the text itself. To stop this, I would end quotes at the end of the page, and then copy and paste the rest of the sentence/phrase from the following page into the quote – which seems fairly inefficient. Any suggestions on this welcome!


    • Jo says:

      Hi Kate,

      I think that is pretty much the only fix around right now. As much as I can say, it is at least in part due to the PDF file format, which does not seem differentiate between different areas of text. If you open that file on Skim or Preview, it should also first grab the footnote before grabbing the text on the next page.

  4. Dellu says:

    Great article, really!
    It is true that Sente has the best annotation system in the town; and I am thinking of buying it just for that feature (Mendeley can do most of the other jobs, even better and plus for free). With all elegance and beauty, there are a few disturbing problems I am facing right now:
    1. Importing from other reference managers: pdf attachments are not maintained. I can import all my references from Mendeley and BibDesk, but all the pdf attachments are ripped off.
    2. Working with Latex is at its infancy stage in sente: most academicians in the science streams use Latex. Even if sente can export to Bibtex format, it would have been better if it can live sync to bibtex files.
    3. Broken links. This is the real series problem with Sente. Many people have already faced this issue. If you moved Sente library to a new position, or you stored your pdf outside of the library bundle, or just renamed the files, the link between the pdf and the annotation gets easily broken. This way, I lost all the annotations of some of my pds in a fraction of seconds. That is very sad and disturbing to me because I don´t want to lose my annotations that I will be working on for the next 4 years (I am staring up my PhD) just in a small mistake.

  5. Dellu says:

    Oh, I forget to mention the other great use of Sente:
    All the notes and quotations in Sente can be exported to Devonthink….very neat!
    I love this feature

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    I tried accessing the various Sente links found throughout several blog posts, however, I continue getting an error that says Sente is not available in the US iTunes store…thoughts?

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