Before, I wrote a few complains (https://dellu.wordpress.com/2016/03/28/where-bookends-sucks/) I have on Bookends as replacement for Sente. It has been almost 9 months since that post.
Now, I am updating my experience with the Bookends.
The good news: the latest version of Bookends (12.7.7) has solved one of the major complains I had on the application. That is: it can now extract references from a plethora of sources that the source of extraction is no more a problem.
In addition, I learned in the course of the previous months that the right method of finding references of PDF books is to use the ISBN associated with the books. Once you write the ISBN of the book in the ISBN field, Bookends happily can download all the reference data from Amazon using its Autofill feature. The Autofill feature is a super-feature. One day, I put about 400 PDF articles collected over the years into Bookends watch folder; all of them have their DOIs printed in the first pages of the articles. It was just magic to see all the PDF files find their references filled automatically in a couple of minutes.
I also leaned that Bookends is much potent application than Sente when it comes to managing references. The tools embedded into it are unbelievably rich. It has organizational tools like: smart folders which support REGEX, static folders, labelling (color coding). It has a fully configurable Format Manager which enables the end user to import or export; rename the references in endless ways. The Format Manager in Bookends is the greatest feature I have ever seen in any reference manager. It is a dream come true. It is a liberating feature. I cannot say enough about it.
Bookends has other tools under Global Change. Finder replace that works across the whole library; batch changing of reference types, batch inserting data..and, other many types of manipulation tools.
Attachment handling and file renaming is superb in Bookends. The best part is: files are managed very transparently. You can explicitly put your files in a Dropbox folder without any hassle: while still they are attached to their references.
The Duplicate Finder tool embedded into Bookends is the best in the class. Jabref is great for finding duplicates. But it cannot reach the complexity and elegance of the duplicate finder in Bookends. You will never miss a duplicate with it.
If you are into Latex, it is also one of the most Bib friendly non-bib reference manager. It can assign unique Bibtex keys: and, the Format Manager can be manipulated to export in any of the Bibtex formats (Bibtex or BibLatex). You can also manipulate your format to export distinct (unique) bibtex fields. You don’t even need to export the reference to get your bibliography to work with Latex. You can make Bookends to work with your Latex file directly.
Bookends has AppleScript dictionary. That again opens a world for who are into the scripting.
Integration with other super applications: I have never seen any reference manager as flexible as Bookends (I admit, Zotero could be even more flexible: I just don’t like that app; never tried it seriously.). For me, the fact that Bookends works well with Devonthink and Tinderbox is the best part of the story. Bookends is hand in glove with both Devonthink and Tinderbox. You can export and import in both directions; you can even directly sync them using some scripts (all the three are scriptable). Combining the three power tools is the nirvana for the knowledge worker. The world has never been greater.
The only feature I am still missing from Sente is the reading and annotating capabilities of Sente. The reading experience in Bookends is nowhere closer to Sente. Otherwise, as I am more using Bookends more, I am getting more surprises how a reference manager could be so rich and so capable. In an ideal world, BE would incorporate the annotation tools of Sente.
Dellu 
I appreciate your writing about this. I love Sente (first used Papers 1,2, and then abandoned it after paying for version 3). I have been unsure about moving to Bookends, esp. since I am in the middle of dissertation writing, but I am really concerned about Sente going belly up.
I was also very happy with Sente. While I still consider the annotation tools of Sente much superior, I think Bookends has some great features. It is amazing tool of automation. I am also at the middle of my dissertation. After many years of hard work–using Mendeley, then Sente, I finally have a truly clean library I can just cite without worrying of the citation is complete or not.
Can you elaborate more on that? “You don’t even need to export the reference to get your bibliography to work with Latex. You can make Bookends to work with your Latex file directly.” As far as I know you still need to export your bib file from Bookends, though
I was thinking about two approaches you can use BE for Latex.
1) you can directly copy and paste the citation keys from BE to the Latex editor (CMD+Y does also work). Then, copy the cited references (using collections, or tags to filter them out), using CMD+K and paste them to your latex editor. You can think of the the CMD+K as a form of export. But, I think this is a simpler process: for simpler papers, it works just fine without exporting them.
2) You can also use tools like BibQuery (or, any script: https://www.alfredforum.com/topic/8817-bookends-search-and-citations/) to insert the citation keys from BE to the editor.
Check my workflow, whether it’s more useful: (1) Use CMD+Y to paste reference key to LaTeX editor, I use Sublime Text; (2) Drag and drop this given reference from All (refs) to a static folder of your choice in BE (3) Use my script below to export static folder to Bib file. To use the script, first select static folder, then select Biblio Bibliography to select folder:
tell application “Bookends”
activate
delay 1
end tell
tell application “System Events”
tell process “Bookends”
keystroke “h” using {option down, shift down, command down}
delay 1
keystroke “a” using {option down, shift down, command down}
delay 1
end tell
end tell
tell application “System Events”
tell process “Bookends”
keystroke “b” using {shift down, command down}
delay 1
keystroke return
delay 1
keystroke return
delay 1
keystroke “r” using {command down}
delay 1
end tell
end tell
tell application “Sublime Text”
activate
end tell
Let me know if you have any questions. By export this script as an app, then put it beside your BE in the dock.
Write your project with steps 1 and 2. When you’re ready to compile do step 3.
Bookends fully formats and creates the bib file, no need for another reference manager.
Thanks for the script. I am playing with it. I will see if I find it functional with my workflow.
I’m thinking of switching to Bookends from Sente. I too am in the midst of my dissertation and uncertain about Sente. Have you any notes or insights on the transfer process. I’ve read the notes on Bookends website. I understand my quick tags will not transfer but my annotation notes do (except for images). Additionally, can you tell me if when the transfer is complete to Bookends, does it leave Sente functional and in its original state?
I am sorry, I didn’t reply you on time.
Yes, the transfer doesn’t affect the original Sente library. You can use both side by side. I even tried to use a common pdf library while keeping the references in both managers. It is doable. But, you have start from Sente. You can keep the Sente Attachement inside the Attachement folder inside Bookends. Bookends has some amazing magic to find the attachments. but, that might be too much of a hassle for you. It is best to completely move to Bookends: or stay in Sente.
For the Quicktags (heirarchial tags), yes, BE has recenlty introduced them. But, the ones from Sente will not be mapped. They will be flattened. You have to do it again.
Other informations are pretty much maintained. I didn’t lose any relevant information except the highlights of the Pdf files. You will have the annotations in BE: but the annotations go as notes. They are not directly linked with the highlight of the PDF. If you want to see the highlights, you have to individually export the PDF files from Sente–which is painful experience as Sente has no batch exporing mechanism.
Thank you for the response. I’m about halfway through the transfer and seems to be going well. While Sente continues to work, I know without continued development one day it won’t. My work is much too valuable to risk. I want to make the transition now while everything works on both sides of the transition. I tried BE ten years ago, while good, I was drawn to Sente’s note taking ability. Well, BE has obviously grown up and look forward to using it full time as soon as I complete the transfer. Again, thank you for your comments.
Yes, I also tried and dismissed BE. the annotation capabilities of Sente are obviously more attactive than BE. But, in the long run, BE turn out to be extremely efficient machine. The tools emebedded in it are so rich and amazing. Good luck with the transfer.
Bookends doesn’t work with web of science that is the heart of papers (at-least for my work)
Why? Web of science is one of the native search engines in Bookends.
I loved Bookends. But I could never seem to get it to work properly with Google Scholar (from which I get many citations for humanities articles). For whatever reason it would always return either garbled or merely reduced (e.g. missing volume and issue number of an article) information that other citation managers (e.g. Sente or Zotero) would get fine. I’ve moved to Zotero, which has better bibtex management. But I think about going back. Have you any experience with Bookends and Google Scholar?
yes, BE used to miss some of the fields. But, I think he has fixed it in the latest version. I am also in the humanities. But, I have sworn for myself not get reference from Google scholar anymore. There is always something missing–the page numbers of artciles, addresses of the publisher etc.
My strategy is to rely on other sources: Jstor..and the original publishers for article. I use Worlcat and university libraries for books.I have learned that all the references I collected from google scholar, using Sente, and specially Mendeley are all so incomplete. It took me ages to clean them all up. It is better not to have a reference than to have an incompelete version of it.
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Yes, the transfer doesn’t affect the original Sente library.
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Yes, the transfer doesn’t affect the original Sente library.
Hi, thanks for this, I was thinking abotu moving to bookends since mendeley is causing me headaches as I now write in scrivener – I’d love a pointer to a page on integrating devonthink and bookends. I thought you couldn’t play around with the devonthink database, but I’d love to be able to download a pdf and get it into devonthink and linked to bookends, and links you have would wonderful (sorry if I have missed them).
I’ve just switched from Sente to Bookends and use both Scrivener and DevonThink. I’ve used an iCloud folder for my attachments (Bookends folder in iOS). My attachments are available in Bookends on both Mac and iOS. Then I’ve indexed the Bookends attachment folder in DevonThink. Search in DT will find article in Bookends attachment folder. Seems to work, but since I’m new with Bookends this may not be the best or only way to accomplish this. When you work this way its important add files through BE and not simply toss them into the indexed folder. Again, others may be prompted to share with you a better way to do this.
There is no easy alternative of doing it. We have been discussing this in Devonthink forum about this. There is one strategy I have suggested for the people who want to directly import their files to Devonthink; and, then associate it with BE.
But, I have never tried it myself: and, could be hard to maintain in the long run. I encourage you to try with a sample data first. It could screw your database. You can look at the original discussion here: http://forum.devontechnologies.com/viewtopic.php?f=2&t=23363&p=116133#p116133
The indexing the folder is the simplest and safest way to use BE and Devonthink. You should not try unless you really understand how the database in Devonthink and the attachement system in BE work.
I’m in the process of moving. My biggest problem is how to move to BE while maintaining my references grouped as I have them in Sente, where I group with tags…and then syncing with iOS BE still maintaining them grouped…
I would love to hear anyone’s IPad worflow who has moved from Sente. I’ve been poking around the Bookends forum, and it seems like Bookends will not allow you to seamlessly read and take notes/quotes on the ipad for later export? With Sente I would take all my notes on the IPad, then run a script on my mac to put them all as rich text files into invidual folders, which would then be indexed by DevonThink. Any ideas or work arounds? Thanks!
Bookends adds standard Acrobat annotations. Yes, you can export them using any pdf reader capable of exporting annotations. Skim offers much control using export termplates. Open the annotated PDF in skim; convert the annotations and export them using a template (rtf; or markdown).
But, if you want individual folders (files) as in Sente exports (i used to do the same, by the way), skim cannot do that. none of the applications can export into separate files, actually. Highlights app was the closest to that kind of workflow. but, the app is buggy and seems abandondened.
so, I think the best option is to export the annotations as a single file and break them into pieces using some script.
Bookends just got even more powerful, since it gained full scripting support (with v13.2). This greatly helps to develop custom workflows or integrations with other apps. For example, you could write a script that exports all your publication’s notes as individual files/database items to DEVONthink.
For more info on scripting Bookends, see my “Scripting Bookends” guide on the Bookends web site (which is also available at: https://extracts.github.io/mac-scripting/Bookends/Getting_Started).