The Great Migration: Moving from Sente to Bookends Reference Manager

The writing was on the wall for a long time, but I didn't want to believe it. I have been using Sente as my reference manager for over 5 years and loved it. But over two years ago, the developers stopped blogging. Then over a year ago, the forum closed down. Then the support emails stopped. It kept working, including its syncing feature, and I hoped that perhaps the developer was just on an extended vacation. Recently, I held my breath as I updated to High Sierra and updated to Mellel 4. Still it worked. But then the syncing stopped. In a last-ditch attempt, I tried again to contact the developer – I even found a phone number online. No luck. I could delude myself no longer. I had to migrate.

Luckily, I knew that I had a wonderful option. Bookends has been a high-rated reference manager for many years, I am even a former user. And the developer of Bookends, anticipating the demise of Sente, has improved its ability to import references from Sente. But despite this all, I still had to put in a lot of grunt work to get all of my information, and especially my PDF highlights, into Bookends.

For those, like me, who are now making the move to Bookends from Sente, here are the steps I had to go through. Before I get to that, a few other comments.

Things that I will miss from Sente

• Being able to double-click and go into a full window reading view was excellent, as was the ability to open a tab to browse. *edit* The recent release of Bookends 13 added a full screen reading ability, which I'm very happy about.
• Attachment and Annotation. By far this is my biggest lament, but I am already adjusting to Bookends and the way it does things.
• While I will get used to and enjoy the notecard stream, in particular being able to add tags and be able to cite directly from them, Sente had a custom highlighter and notes that remains unparalleled. Being able to quickly choose to quote and choose the color was in a pop-up immediately when highlighting was excellent.
• The Bookends notestream is quite different and will take some getting used to. I imagine that former Sente users will most use the “Highlight Selection and Make Bookends Notecard” from the annotations menu. What remains somewhat clunky in this process, in my opinion, is that this creates 2 notecards, one to links to the PDF (so you can jump to the spot) and the other the actual notecard to take your notes. I so wish these were combined into a single item so that the note stream wouldn’t be cluttered. This can be hidden in the annotations menu at the bottom, but  clicking on the notecard doesn’t jump to the spot in the PDF. Thankfully, you can still jump to the notecard spot in the PDF via a shortcut key, or by right-clicking the notecard and choosing "Find in PDF."
•  Whereas Sente had the automatic layout for title, page, quote, and notes, only the page and quote are automatic in Bookends. For the rest you need to learn the syntax Bookends utilizes. And unless I’m doing something wrong, Bookends doesn’t know automatically which page is being cited, it takes the page of the PDF, rather than the actual page number (pulled from the page range). This creates extra work.  *edit* The recent release of Bookends 13 has changed this functionality to reference the actual page number, which is fantastic.
• Sente’s auto-links were beyond wonderful and helpful. Auto-links built off of the DOI or ISBN, this was a great way to see other web metadata and especially being able to do a book search in google books.

Bookends Features that I Look Forward To

I actually started out as a Bookends user so I am very familiar and like the app. I have never had any hesitation in recommending Bookends to people. The above issues are the reasons I ultimately moved to Sente. But since my departure from Bookends, some additions have been made that I look forward to utilizing or making use of again.

• Bookends importing has always been better than Sente overall. The Bookends Browser works extremely well and I am very happy with it.
• Bookends has always worked amazingly well with Mellel, my Word Processor of choice. The integration has only gotten better over the years.
• Bookends does cloud sync with iCloud now, and has added a very nice iOS app. Of course this means that I have to rely on iCloud syncing which isn't always 100%, but that is getting better too.

My Steps For Migrating Data from Sente to Bookends

 

Step 1: Duplicate your Sente library for safe keeping

Duplicate your Sente library, as the steps below will slowly delete items from the Sente library.

Step 2: Prepare Bookends Library to match your Sente library

1. Replicate your “Sente Statuses” from the Library setup in Bookends preferences>Lists
2. Replicate your bookmarks from “Web Bookmarks” from the Library setup in the Bookends bookmarks found when you click on an item and open the Browser
3. Replicate your Sente reference types in Bookends preferences Refs>Reference types (I recommend  not changing any - leave those that are there, and any new ones you need)
4. Replicate your Sente Reference Type fields for any special fields you may use
5. Decide how you want your PDFs named. Unlike Sente, which does a really nice folder hierarchy, Bookends places them all in a single folder. I created a simple format file for Bookends to use the last name date - short title for all attached PDFs.
6. You can customize the summary view in the Preferences to look how you would like it. (I’m happy with the default, but may create my own format for the summary view in the future)

Step 3: Confirm your Attachments

Unfortunately for some of us, Sente may have done us wrong at some point – or the use of multiple computers might mean that some of your attachments aren’t on the computer you are using for the migration. Hopefully none of them are MIA (i.e. sitting on Sente’s now-defunct server). If you have some missing, make a list of them in some way (static group or a bibliography) in order to check another computer.

Step 4 (optional) : Attachments

People will need to decide if they are happy to keep the notes/quotes made without them being linked to the PDF. When importing directly from Sente to Bookends, Bookends will bring all of the notes over into its notestream, but the highlights and connection to the PDF in Sente will be stripped, as this was stored in a special way in Sente.

After thinking about this, I made the decision to put in the grunt-work of keeping my highlights for the bulk of my PDFs. The result was the following process:

1. Scan through your Sente library. Whenever you find an entry with the attachment and notes icon, I added a quick tag.
2. I then imported this group into Sente, and then went through each one, adding new highlights in Bookends. After doing this, I deleted each item from Sente.

Step 5 (optional): Set up Sync

1. If you want your library and attachments cloud synced and available on your iOS devices, you need to purchase the app, then purchase the yearly subscription.
2. In Bookends you will see a cloud icon to sign in to iCloud and enable the sync. If you have lots of PDFs you will need to pay for additional iCloud storage as well. Alternatively, you can use another sync service (dropbox, google drive, etc.) for your attachments and custom folders.
3. Alternatively if you do not have iCloud, you can also sync Bookends over wifi.

Procedure for Moving Library Over

Keep in mind that the things which do not get transferred over are Sente statuses (Bookends labels) and the reference type does not always come over correctly, particularly for special citation types that you may use. You are safe, as far as I can tell, with the standard Books, Book chapters, edited book, journals.

Bookends has made it very easy for Sente users to import. In Bookends, go to File>Import>from Sente and click okay. Then highlight the items you want to import in Sente and click OK on the little dialogue button you will see.

1. I highly recommend that you take 1 of each type of reference in your library and import it to Bookends. Inspect and make sure that all of the info came over and into the expected fields. For the most part this should be fine, but if you have customized Sente, this may complicate the process. In my case, dissertations didn’t bring the info over correctly. Luckily, Bookends is amazing and mass changes, and I was able to correct the problems quickly.
2. First move over from the group you’ve made for Attachments (see below). Move them over by status>type to ensure that they get moved over as the right type of citation. Upon bringing them in, THEY WILL BE HIGHLIGHTED. IMMEDIATELY use the correct shortcut to apply the label necessary. there is no other easy way to mass change labels later.
   **As an alternative, you can use temporary tags in Sente to mark your labels and different Reference Types. This would allow you to import your entire Sente library at once and then fix your labels and reference types doing a search for those temporary tags in Bookends. The reason I chose to do it this way (i.e. without the temporary tags) is to minimize the chance of import errors which can occur from time to time.
3. Go back to Sente and delete each of these imported citations to remove them from the database.
4. Once you are done with these in the group, go to the folder with the exported PDFs on your desktop, and attach each of them to the correct citation.
5. Now continue the process through your status groups, bringing them in by type to ensure they come through correctly by type and immediately assigning the label. The easiest way to do this is to use the Status filters on the right and then using Sente’s list view and click on the Type column to organize them by type.
6. One other thing I noted during the process is that at times some “stray code” came in as attachments. This may not bother people, but it annoyed me. So I had the added process of going through Bookends and whenever there was a double paperclip icon, I went in the BE Inspector to delete the stray code attachment.
7. Bookends is great at doing mass find and replaces. One thing I needed to do was replace ^{with ^, and} with ^ . This is how superscripts are indicated in Bookends. Any ampersands come through as “&amp;” so replace those as well. In my abstracts and notes I frequently used line breaks, which come through as <br>, so I replaced them.

Those are the steps I took. I've unfortunately had to spend an inordinate amount of time on the process, but it is done and I'm now the proud user of Bookends.

Pt 2- Why Academics & Students Should be Using a Reference Manager: app roundup

In my previous post I highlighted the six reasons every academic and university student should be using a Reference Manager. In this post I will highlight some of the top apps out there in this category. I have had hands-on experience with most of these apps at one time or another.

As I have taken some time to research these apps for this post, I have come to realize how level the playing field has become. At one time, Endnote stood out as being the best integrated with MS Word. At one time, Zotero was popular because it was free and could flawlessly pull in citation information from pretty much any website. At one time, Papers stood out as the interface to beat on Mac. At one time, Bookends stood out as having the most robust formatting (which is important for those of us enslaved to the Turabian method). At one time, only 2 or 3 of the apps had built-in annotation abilities for PDFs.

This isn't the case anymore:

• most are now fairly flawless when it comes to formatting.

  • This was not the case only a few years ago. A number of these apps arose out of the hard sciences scene that uses APA, which is a much simpler formatting style. This meant that a number of them weren't equipped for Chicago/Turabian/SBL formatting. This isn't the case anymore.

• most have built-in annotation abilities

• most can now effortlessly pull citation information in from the web, usually from within the app itself

• All of them now integrate with MS Word, and a few add other word processors into the mix as well

• Many of them now have collaboration abilities

In addition to what are now the staples for this category, we can add the cloud-syncing that is now the norm for most of them. The cloud-syncing has opened up both web access and mobile apps as well – I now carry my entire library around on my iOS app, and can read and annotate any PDF article I have on the go as well!  Academics have some truly helpful and powerful technology at our fingertips.

Below I spotlight 10 Reference Manager apps in no particular order. After a brief summary, I evaluate a few of them based on particular items (cost, platforms, etc). There are many more than 10 out there, but these seem to me to be the most popular and most-used. Hopefully you will find one of these useful. If you do decide to adopt one of these, I highly recommend taking the time to study the manual and watch video tutorials – become a master of that app, as it will pay rewards in your life later.

*full disclosure: I receive a small affiliate commission for some of the links below. If you do purchase through these links, thanks!

BOOKENDS

www.sonnysoftware.com    (AppStore link)

This is my current reference manager of choice after the demise of Sente. My very first Reference Manager was the now defunct RefCite on a PC. But just after starting to use that, I switched to a Mac and never looked back. Once on a Mac, I stumbled upon Bookends. Bookends was also the focus of my first academic-ish type article on the SBL Forum. Bookends is one of the fastest in terms of searching your own database, and its built-in web search is great. Bookends is also, still, one of the few Reference Managers that can do global changes like find & replace. Bookends has enhanced functionality with Mellel, which is my Word Processor of choice (why not MS Word? In addition to being clunky and slow as molasses with large documents, MS Word on Mac STILL doesn't properly handle unicode right-to-left Hebrew!) and handles SBL format well. I also appreciate the very responsive support by its developer. Bookends has continued to evolve, with built-in PDF annotation, syncing via iCloud, a mobile app, and great note-taking abilities.

• Cost: $59.99

• Platform(s):

  • Mac

  • iOS app

• Sync: via iCloud (and settings via Dropbox)

• Word Processor Compatibility: MS Word, Mellel, Pages, Nisus Writer, Open Office, RTF documents

• Formatting: Uses its own formatting interface. Comes with hundreds of format files.

• Document Annotation: Built-in annotation, saved directly to PDF. PDF notes are saved in the Bookends note-card system.

• Strength(s): very responsive developer. Excellent integration with Mellel. Very fast database searching.

• Weakness(es): No collaborative abilities. No collaborative features.

ENDNOTE

www.endnote.com

Endnote has been around the longest. I wasn't around when Reference Managers first made their debut, but I think I'm correct that Endnote invented the app genre. It has continued to evolve and is still the dominant player on the market – it continues to be the only app that is natively supported by MS Word and Apple Pages (fyi, I wish Apple would make this more open for other developers). Endnote works great with MS Word, and it has widened its reach to include Mac, iOS, and the web. Endnote also has collaboration abilities. While many decry Endnote's cost, student cost isn't that bad, and the apps that charge year to year actually cost much more in the long run.

• Cost: $249.95, $113.95 for students

• Platform(s):

  • PC

  • Mac

  • iPad app

  • Web

• Sync: Built-in cloud sync. Collaboration and sharing with colleagues enabled.

• Word Processor Compatibility: MS Word

• Formatting: Uses its own formatting interface, many pre-built formats available for users.

• Document Annotation: Built-in annotation and note-taking that is written to the PDF.

• Strength(s): MS Word integration. Multi-platform. Huge community.

• Weakness(es): Works with MS Word only.

PAPERS

www.papersapp.com

Papers popped up in the void of a good Mac PDF manager. Initially Papers was more about finding good references right within the app (mostly for the hard sciences) and enabling annotation and note-taking with the PDFs. Papers continues to have a great user interface and has evolved to be a full-fledged Reference Manager that handles citation and bibliography generation. It has also expanded its reach on to PC and the web, which enables collaboration abilities. Papers continues to have one of the best interfaces, and continues its aggressive development. I am unclear on how Papers handles journal abbreviations (us Biblical Studies guys need to use abbreviations in footnotes, not in bibliographies. Sente, Bookends, and Endnote do this well).

• Cost: $79

• Platform(s):

  • Mac

  • PC

  • iOS app

  • Web

• Sync: via Dropbox

• Word Processor Compatibility: MS Word, RTF documents

• Formatting: Uses the CSL repository - http://citationstyles.org

• Document Annotation: Built-in

• Strength(s): Ubiquitous. Aggressive development. Great interface and built-in searching. Particularly large hard sciences user base.

• Weakness(es): Limited word processor integration

MENDELEY

www.mendeley.com

Mendeley has made quite a splash in the Reference Manager area and has really raised the bar in terms of cloud-syncing and collaboration. It continues to stand out, in my opinion, as being the most collaborative and social of all of the Reference Managers. Its 2GB free policy really encouraged (forced) many of the other apps to add collaboration, cloud-syncing, web interface, and even a free option. For students who aren't necessarily going the academic route and don't want to spend anything, I tend to recommend Mendeley. Its interface is fairly simplistic and easy to understand for beginners, and what it does it does very well. As far as advanced features for research, I find it a little lacking – but I'm a bit of a tech junkie.

• Cost: 2GB free (annotations not synced), 5GB at $55/yr, 10GB at $110/yr, unlimited storage at $165/yr

• Platform(s):

  • Mac

  • PC

  • Linux

  • iOS

  • Web

  • 3rd party Android apps

• Sync: cloud-based

• Word Processor Compatibility: MS Word

• Formatting: Uses the CSL repository - http://citationstyles.org

• Document Annotation: Built-in

• Strength(s): Collaboration abilities and paper-sharing community. Good document annotation. Free.

• Weakness(es): Recurring cost. Not as full-featured as others.

QIQQA

www.qiqqa.com

Qiqqa is not super well-known but that doesn't mean it shouldn't be. Qiqqa first stood out to me as I was looking for a PC alternative to DEVONthink (a great Mac research database). Qiqqa started out as simply a PDF manager, enabling great annotation, note-taking, and searching of the PDFs. Qiqqa continues to do this better than any program, in my opinion. Since I last looked at it, it has, like Papers, now become a full-fledged Reference Manager that can manage your in-text citations and bibliographies. If you are on a PC, I'd highly recommend checking out Qiqqa. If I were a PC user, I'm fairly certain this would be my Reference Manager.

• Cost: 200mb free (ad-supported). 8GB at $72/yr, 50GB at $240/yr

• Platform(s):

  • PC

  • Android

  • Web

• Sync: built-in cloud syncing

• Word Processor Compatibility: MS Word

• Formatting: Uses the CSL repository - http://citationstyles.org

• Document Annotation: Built-in

• Strength(s): PDF handling and note-taking. Collaboration abilities.

• Weakness(es): Recurring cost. Platform limited. Works with MS Word only.

ZOTERO

www.zotero.org

Zotero is a favorite for many, and for good reason. Zotero started out as a Firefox plugin, and this origin highlights one of its main strengths - it seamlessly integrates with your web browser and flawlessly pulls in information. It was Zotero that really pushed the others to start pulling in information from the web too. Like Mendeley, it is free for a certain amount of space. I never really warmed up to Zotero's interface and don't like that it doesn't have PDF annotation built-in – but given the playing field, this may change soon.

• Cost: 300mb free. 2GB at $20/yr, 6GB at $60/yr, unlimited storage at $120/yr

• Platform(s):

  • Mac

  • PC

  • Linux

  • Web

  • 3rd party iOS apps

  • 3rd party Android apps

• Sync: cloud-based

• Word Processor Compatibility: MS Word and LibreOffice/OpenOffice/NeoOffice,

• Formatting: Uses the CSL repository - http://citationstyles.org

• Document Annotation: none

• Strength(s): Web importing. Collaboration abilities. Huge user base and community.

• Weakness(es): Recurring cost. No mobile app. No document annotation. Works only with MS Word and OpenOffice.

CITAVI

www.citavi.com

Citavi is quite popular in Europe, not as much in North America. Citavi focuses a lot on the knowledge organization side of things, with task management and note-taking. Citavi is unique in that its formatting is all built-in and if you need a new format, the developer makes them. You can collaborate with a special version of Citavi.

• Cost: $156

• Platform(s):

  • PC

• Sync: no

• Word Processor Compatibility: MS Word, OpenOffice, RTF documents

• Formatting: 3,000 Built-in formats. Developer-built only.

• Document Annotation: none

• Strength(s): note-taking and knowledge organization. Task management.

• Weakness(es): No mobile app. No document annotation. No sync.

BIBLIOSCAPE

www.biblioscape.com

Biblioscape is another PC-only option. Like Citavi, it has a strong emphasis on knowledge organization and note-taking. Its interface, like Citavi, is pretty dated with that Windows 98-type feel. You can collaborate with an upgraded version.

• Cost: $149

• Platform(s):

  • PC

• Sync: no. But Biblioscape can run as a server on your network, and allow others to view your database.

• Word Processor Compatibility: MS Word, RTF documents

• Formatting: Uses its own formatting interface, many pre-built formats available for users.

• Document Annotation: Built-in.

• Strength(s): Strong emphasis on note-taking and research. Task lists and chart-making abilities.

• Weakness(es): No mobile app. Poor interface. No syncing.

REFWORKS

www.refworks.com

Refworks continues to be web-only, which is good for some and not-so-good for others. This allows for some collaboration abilities and has a mobile-friendly web interface.

• Cost: $100 / yr

• Platform(s):

  • Web (mobile friendly)

• Sync: no

• Word Processor Compatibility: MS Word, RTF documents

• Formatting: Uses its own formatting interface, many pre-built formats available for users.

• Document Annotation: Built-in.

• Strength(s): Strong emphasis on note-taking and research. Task lists and chart-making abilities.

• Weakness(es): No mobile app. Poor interface. High cost.

I have tried to be as accurate as possible. Please let me know if I have made any errors and I will update the post. As I said in my previous post, a Reference Manager can be one of the most important tools for an academic.

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Pt 1 - Here is Why Academics & Students Should be Using a Reference Manager

Books. Journal articles. Essays. Conference papers. Websites. The job of the student and academic is to swim through and manage a sea of reference material. And the waves of information and material has increased. Lucky for us, technology has indeed kept up with this need. Word processors are better than ever. Computers are faster. More is available online. In this post I want to introduce you to the one type of app that I think every academic and student can utilize to help manage academic literature: the reference manager.

There are quite a number of reference managers out there, all of them quite good. You may have heard of Endnote, or Mendeley, or Zotero. But you're not quite sure what they do. In this post, I will explain exactly what a Reference Manager does. Once I do, you will immediately see the value. In a subsequent post, I will briefly list and describe some of the reference managers out there.

Here is the six main things a reference manager does for you:

1. One place to keep all of your info. Previous to the advent of the reference manager, a well organized academic kept a massive text document of all of their books, essays, journal articles, etc. Within the document they would make sure it was properly formatted for the bibliographic style of their discipline. A reference manager provides a convenient place where all of this citation-type of information (i.e. metadata) can be stored. The prevalence of Reference Managers has made the collection of this information exceedingly easy. You rarely need to type in the information manually anymore.

2. Organize the info with groups, folders, tags, keywords, etc. Building off of one consolidated place to store this citation information, a Reference Manager now allows you to add your own data to this information. Tags/keywords can help you to quickly find information on particular subjects, and groups/folders can help further organize into categories, projects, etc.

3. Keep PDFs with its Info. The majority of journal articles are now online and many of us choose to download a PDF copy of the articles. In addition, it is easier than ever to create a PDF scan of book chapters, or create a PDF copy of a webpage. A Reference Manager allows you to keep a PDF of an article together with its information. No need to have complicated folder structure, or go searching through your documents folder.

4. Take Your Reading Notes in One Spot. Back in the days when all I read were print books, notes on the back pages or sticky notes were the norm. But even then, this style of note-taking was limited and stuck on my shelf. Now, with so much material being consumed on our computer screen, Reference Manager's have made it easy to take notes and highlight information right alongside our PDFs. Your notes are now attached right to your citation information. Many Reference Managers also provide a way directly within the app to take notes and highlight a PDF directly.

5. All of This Stuff Above – Search It! Now we're getting to the "power" of the Reference Manager. Not only has it provided you with a convenient place to store and organize your citation data and documents, but all of this information is now searchable. Your library's usefulness has been super-charged!

6. Automatically Generate Your Footnotes & Bibliography. Read that sentence one more time, and let it sink in – REFERENCE MANAGERS WILL WRITE YOUR FOOTNOTES AND BIBLIOGRAPHY FOR YOU! I remember well the day I was sitting in the study room, frantically trying to properly footnote all of my citations in a major paper, and my OT prof Glenn Wooden walked by. Perhaps seeing my agitation, he asked what I was doing. Once I told him, he said, "you know there is software that can do that for you, right?" This actually marked a huge turning point for me. I wasn't tech savvy before that moment - now I'm a tech ninja! And it was because I realized how using computer apps could actually make my life easier. Every Reference Manager works with word processors (like MS Word) so that with a few clicks of the button, you will be properly citing your sources and creating perfectly formatted footnotes and bibliographies. You manage the data and make sure it is in your Reference Manager correctly, and let it worry about the formatting.

There are your six main reasons you should be using a Reference Manager. Perhaps there are other great reasons I haven't thought of – if so, let me know in the comments. If you aren't using a Reference Manager yet – now is the time!

Part 2- Reference Manager Round Up

photo credit: libraryman via photopin cc