Bookends vs. Endnote

Hello everyone,

After hearing raves about DEVONthink Pro, several days ago I downloaded the trial edition and by the end of the day, I was so delighted that I purchased a license. Amazing software, and I’ve only scratched the surface.

Splendid forum, too, about matters DEVON and beyond. I’ve read many positive posts about Bookends; many of you seem to base your scholarly workflow around both Bookends and DEVONthink (with a word processing software - I’ll ask about Mellel in a future post). For years I’ve used Endnote and recommended it to my thesis advisees, thinking it was the only game in town. It’s been reliable, if a bit clunky. I’ve downloaded the trial version of Bookends, and I do like the look of it (and it’s temptingly easy to transfer everything from Endnote!). But before pulling out my credit card and learning a new system, I’d be grateful to hear from users familiar with both programs about the pros and cons of each. I foresee using DEVONthink for taking research notes as well as storing journal articles, archive websites, and my own conference papers and articles, but I’ll still need a dedicated bibliographic database (I’m a literature professor). How, precisely, do you integrate your use of Bookends with DEVONthink?

Thanks for your ideas!

I am not a bookends user, but am interested in the integration questions susan asked. Besides what susan mentioned about learning a new software, I also decided to stay with endnote after considering the time in transferring the custom reference formats I’ve created over the years.

A little off topic, but related: I’d take a steep learning curve and recreation of reference formats in another bibliographic software. if it was possible to integrate existing bibliographic databases in DTPro. Is it just a dream?

I must say that I have never bothered with bibliographical softwares, and just entered my references as text, first in Filemaker and now in DevonThink Pro Office.

A year and a half ago, I moved to Bookends after years and years with EndNote for Windows and then EndNote for Mac. About six months ago, I moved back to EndNote. Reasons:

(1) I had to spend lots of time fixing the citation formatting in articles I had written with Bookends. This is not to say that its formats are less well designed, or that its formatting language is less capable, than EndNote’s; but after all those years with EndNote, I had my usual formats nicely polished, and I just didn’t want to spend that sort of time tweaking the Bookends style. Whether this would like be a problem for you may have to do with your discipline. I’m in the humanities, where the footnotes involve full first and short subsequent citations, not just author-year styles. (This is why merely using just Filemaker or DT would not work well in the humanities: the important part is not generating bibliographies, but generating formatted footnote/endnote citations.)

(2) With a database of only about 4000 items, Bookends got really sluggish on my Macbook Pro. EndNote X, by contrast, is surprisingly snappy.

(3) Neither program is well designed for those who, like myself, hate using the mouse. But for me, Bookends was clumsier–more keystrokes needed to enter information, more mousing to get to fields inaccessible via the keyboard.

(4) Finally, I found that my needs were not very sophisticated. Bookends’ folders and smart folders are very cool in theory–but my citation manager is not where I do my classifying and searching. That’s work for my notes, which is to say for DT or some equivalent.

To the real question Susan was getting at, I must say honestly that I have wasted hours setting up such integration only to find that it wasn’t very important. In my day-to-day scholarly work, the only integration between bibliographical and note-taking software that I have found useful is a way to get from the citation in EndNote (or Bookends) to the notes I have taken on that source (in DT or equivalent). I am now waffling between DT Pro, which I’ve used for several years, and EagleFiler, in large part for that reason: in EagleFiler, every record has its own URL, which can be used to create links to that record from external software.

That’s the view from a medievalist. Obviously other disciplines, with other habits of work, forms of publication and documentation, conventions of citation, and so on, have different needs. Hope this helps --Steve

I do find EndNote’s formatting language to be easier to read and manipulate, but it could be habit.

Interesting. Did you increase the Bookends cache size? (even though I find it strange that the user has to adjust such a thing – why can’t it be automatic?) I do find Bookends to be slower in general than EndNote.

Only EndNote is cross-platform, so if you need to share your databases between Windows and Mac users, you’ll need EndNote.

While exceedingly useful, Bookends’s UI is not typical of other programs with well-designed UIs. It is improving, however. This can be said of the program in general, which is frequently updated. Currently, it is probably the most full-featured bibliography management program available for the Mac. However, Sente is close behind, and it has a better (and more attractive) UI than Bookends.

You might be interested to know that Bookends 9 and later offers inter-application linking as well (i.e. each record has its own URL).

Exactly–I think that it may be habit in my case as well. I wasn’t claiming so much that Bookends’s language is more difficult to manage as that it was more difficult to manage for me.

I didn’t find that the cache size had much effect.

Ah! Right; I should have mentioned that. For me it is less useful than linking going the other way; since finding a citation in EndNote or Bookends is just a matter of typing the author’s last name, I never have trouble finding getting to the citation from the notes, but it’s more complex getting from the citation to the notes.

I hope I made it clear that I thought Bookends a great program. And it should be said that there could not be a greater contrast between the developers. Jon (of Bookends) is instantaneously responsive, utterly dedicated to his product and his users; Thomson ResearchSoft is…well, you know. And though I’m tryiing EagleFiler, DT is spectacular; I have found that some of its virtues are not useful to me, and there are features of EF that may put it ahead for me (the searching, though rudimentary, works as filtering, which fits my work-habits better; the record URLs are useful; it uses Finder data but allows editing from within EF), but I would heartily recommend DT to anyone.


PS Despite what my “Location” says, mbizer, I’ve just spent the summer in Austin. My, what a hot and rainy town you have!

Well, I’ll probably get banned for writing this, but while DT used to be the only game in town, but there are many viable, even preferable, alternatives. EagleFiler’s developer, Michael Tsai, who also wrote SpamSieve, is wonderful. And have you tried Journler?

Of course you won’t get banned for saying that. This is a user forum. :slight_smile:

Different people have different working styles. I have a writer friend who still uses stacks of 3 x 5 cards for his notes. I used to have shoe-boxes filled with thousands of cards. Now I’ve got more than 150,000 thousand documents among my DT Pro databases and I’m a happy camper when doing research. My databases are topically organized and run up to about 24 million words in a given database. Search speeds are fast and I make a lot of use of the See Also and See Selected Text artificial intelligence features when looking for ideas.

I use a lot of the available features including scripts, smart groups, glossary features and so on.

It’s not bad to have competition. We think the DT applications remain ahead in speed, scriptability, scalability and artificial intelligence support. And major improvements are planned for the future, including very powerful queries, multiple concurrently open databases, Spotlight integration, tagging and more.

Of course, it’s up to users to decide which tools best meet their own needs.


Unless I’m mistaken, unlike in Journler and EagleFiler, there are no true smart groups in DT – they’re applescripts linked to folders which require the user to click on them in order for them to update.

And while the AI features are nice, many users are beginning to find that they get in the way, and that they simply want to tag their entries themselves.

Frankly, it seems that DT is starting to fall behind – other programs already offer up their entries to Spotlight searching and don’t require Leopard in order to be able to have more than one database open at a time.

Speak for yourself. In my experience, manual tagging doesn’t scale to the number of items (or topics) I’m dealing with.

Retrospective tagging especially doesn’t scale. When I suddenly find myself interested in a new area, DTP is much better at finding newly relevant articles in my database than I am. The See Also capability alone justifies DTP’s existence for me.


I respect your experience. I was actually quoting a friend.

I agree that scalability is very important. However, I have to say that I don’t find DTP’s UI to be particularly responsive on my PowerBook G4 1.67 GHz with 2 GB of RAM and a 7200rpm hard disk, running MacOS X 10.4.10. There are perceptible delays when displaying the contents of folders (862 entries), creating a new rich text note, actually displaying an entry in the three-pane view, etc. I’ve performed “Verify & Repair” and “Backup & Optimize.”

As for improvements, I’m frustrated by how long it takes for them to appear compared to competing apps.

Hi, mbizer. I sympathize with your frustration. But the next version will be a major recoding and will need to work well with Leopard – which isn’t yet in final, polished shape.

The responsiveness issues you note are not UI issues per se but RAM/Virtual Memory issues. The next version will reduce memory requirements and will also allow multiple open databases in DT Pro and DT Pro Office – which will of course allow one to use more memory all over again. :slight_smile:

Which means that it’s nice that current MacBook Pros can be populated with 4 GB RAM and MacBooks with 3 GB RAM. Within 5 years or thereabouts I wouldn’t be surprised to see Mac notebooks capable of holding 10, 12, 16 or even 32 GB RAM. Users will then demand features and performance of software that will eat as much RAM as is available.

The database I’m using at the moment has over 25,000 documents and more than 26.5 million words. When I’m working it heavily on my MacBook Pro with 2 GB RAM I start getting lots of pageouts, indicating heavy use of Virtual Memory. Responsiveness then slows. But on my Power Mac G5 dual core with 5 GB RAM I can work the database hard for days without ever seeing a pageout, so a single-term search takes only a few milliseconds and repeated See Also operations are virtually instantaneous.

Hi Susan:

I’ve used both EndNote 9 and Bookends with a preference for Bookends. One advantage of Bookends is it’s ability to link PDFs to the citation in an automated fashion (either searching PDFs on your hard drive or downloading from pubmed). Bookends saves it’s PDF files in an ‘attachments’ folder (Documents/Bookends/Attachments) and the PDF is visible within the program. Endnote 9 required finding the PDF on your hard drive yourself. You would be the best judge of Bookends internet search abilities for the literature field. On the negative side I find Bookends to be slower when working with large databases.
Transferring your reference database (in either program) involves exporting it in the Bibtex format. In Endnote you export (file menu) using the Bibtex.ens output style, then change the file extension to .bib In Bookends you transfer the database to the ‘hits’ group (by using ‘mark all’ in the Refs menu) then use the bibliography formatter (in the biblio menu) to output the hits as Bibtex to disk. In either case you can drag and drop the bib file into Devonthink where the database saves it as a ‘sheet’ including the abstract.
On a periodic basis I sync my references by exporting/importing them (deleting the older .bib) and dropping the new PDFs into Devonthink.

Thank you all so much for your thoughtful replies and for stretching my original post in such interesting directions. And Pascal, I love your productivity blog! In the end I decided to purchase Bookends; I find its interface is more intuitive and welcoming than Endnote’s.

All best,

This is too late to be useful to Susan, but a few points I’d like to comment on.

  1. I think anyone thinking about a reference manager and integrating it with other software should read and reread svg’s post near the top of this thread, and consider what features you really need. While being cautious, it’s also good to be open-minded towards needs identified by developers that users are not aware of or wouldn’t have consciously realised are actual needs.

  2. This may not be the case for academic users in the US, but for me, a former EndNote user, EndNote just became too expensive to continue using. It was cheaper to buy a new Bookends licence than an EndNote upgrade. Most Bookends upgardes are free, and none has been expensive. And anyone interested in Mellel for word-processing should be aware of discounts for a package of the two applications.

  3. Sente does have a very attractive interface!

  4. Bookends now has some integration with RefBase, server-based reference management software. If you’re into sharing references with colleagues, this is a very promising development. The integration is in its infancy, and the developers of RefBase and of Bookends are both very willing to listen to users’ wishes.

  5. There are easy ways to bring your Bookends database into DT. The “low-tech” way is to export the Bookends database as text, perhaps using Ref with Abstract or some such format. The sophisticated way is to export to BibTeX, and then import the BibTeX file, which becomes a “sheet” in DevonThink. Each record in the sheet corresponds to a single record in Bookends, and searches in DT throw up single records as results. If you use OS X Services, you can select a title in a Bookends record, and then use Lookup in DT to go to a search window with the query ready-inserted.
    Because there isn’t any auto-synching, you’d want to be systematic about bringing Bookends into DT. I do it every time I collect 100 references, so I have sheets entitled Bookends001-100, Bookends101-200, etc.[/list]

Thanks for helpful tip about last 100 refs to sheets.

I have a folder for files of notes and scans from books and articles. Each is linked to the bibliographic item in BookEnds, and the folder is indexed by DevonThink.

(Humanities lecturer at a British university).

Dear John,

Could you give me more detail about how you set this up?