What are you using to manage bibliography databases?

DEVONthink Tips
1

I’ve combed through the archives in these fora and note that a number of solutions for managing bibliography have been cited. However, most of the posts on this topic go back a number of years, so the experienced hands here could help a noob by answering a question:

On which bibliography management tool(s) have you settled?

Thanks. Your responses will help me in my quest!

2

I have used BibDesk for porting to LaTeX, but must admit that I tend to do things in a shamefully inefficient manner by having two documents open when writing: the master text file (written in straight text as opposed to a word processor) and a references file.

Yes, this means I’m typing out references manually, but I reasoned a while back when learning LaTeX that the amount of time the ‘manual method’ takes is likely less than the amount of time I would need in fiddling with the proper output bib style in LaTeX. Maybe it’s time to revisit.

I guess I’m still stuck in the old days when all my references as a grad student were on index cards. Still have them somewhere, too…

David

3

I use Sente! It incorporates with Mellel very easily. Mellel took some time to learn but now I am in love with it! And I looked at Sente and Bookends and compared both at the same time by downloading and testing each one back to back. Sente is definitely better!

4

Thanks for the reply.

I’ve been using Bookends with some success. The scripts available for DTPO aren’t 100% reliable for importing bib references. The comments in the script indicate that it’s related to Bookends’ failure to identify its main window.

I also downloaded Sente and started using it, but I’m in a time crunch - editor’s deadline - so the 30 trial will probably expire before I can test it thoroughly.

In the meantime, I’m using Zotero. When all the shouting is done I may settle on that; the price is right.

5

I use BibDesk, a great open-source reference management software package, with the help of Zotero and Zot2Bib, as described in the thread Lit & Note storing in DT and external Bib-Manager. If you use BibDesk (or are considering using BibDesk) you may be interested in the threads: How to index individual BibDesk entries in DEVONthink and Bibdesk keywords => MacOS tags ≠> Devonthink tags.

6

Bookends. Solid and reliable. Never let me down. Unlike some it’s in constant development and the support is second to none. Can’t recommend it highly enough.

I’d be wary of Sente. Many, (even on their own forums), talk of it as being abandoned. There’s been nothing at their site or blog since last December - Just a heads up there.

7

Ditto - Bookends. Highly versatile, scriptable, solid, connects well with DevonThink and can work with BibTex. There is a script that I found somewhere on this forum that connects references in DevonThink with a reference in Bookends. Have pasted it below.

tell application "Bookends"
	try
		set theID to «event ToySRUID» "Selection"
		if theID is {} then error "Nothing selected in Bookends!"
	end try
end tell

tell application id "com.devon-technologies.thinkpro2"
	try
		set theVerweis to ""
		set theRecord to the content record of think window 1
		if theRecord is {} then error "Nothing selected in DevonThink Pro!"
		set the URL of theRecord to ("bookends://sonnysoftware.com/" & theID) as text
		set theVerweis to reference URL of theRecord
	end try
end tell

tell application "Bookends"
	activate
	try
		«event ToySSFLD» theID given «class FLDN»:"User4", string:theVerweis
	end try
end tell
8

I am using EndNote. Its current iteration is quite capable and I appreciate its integration with iPad (importing from Browzine is sweet). It is also surprisingly scriptable and I’ve developed an extensive set of scripts to overcome limitations/idiosyncrasies in my workflow. I have EndNote automatically file my PDFs to a single folder, which I have indexed in DT. One of my Applescripts writes each article’s title, author, publication year and journal to the PDF, which is displayable and searchable in DT. I also have an Applescript to open the EN records of any selected DT records (and another for the reverse), which makes it easy to go back and forth between them. Lastly, I have a smart folder set up in the Finder which shows all of the PDFs filed by EndNote, which is helpful because EN puts all the attachments for a given record in its own randomly numbered folder.

9

Hi, i started with Sente, which I liked a lot. But the Bibtex support was lousy (with respect to special characters etc), so I switched to Bookends which is a nice piece of software with world-class support. But then, after reading many of the superb Bill_DeVille posts, I noticed that I spend a lot of time on the software rather than on reading papers, and I need to cite only a very small fraction of the papers I read. So I now use BibDesk for citations only, with no link to DTPO. I manage/read and annotate my papers/pdfs in DTPO, moving to a Bill_DeVille-like workflow, as has been described in many of his posts. So far I don’t see a real need for me to connect BibDesk with DTPO. Although it is fun to play around with software, I want to see a measurable payoff for the time investment needed.

best
Tom

10

Thanks for reposting this. Very useful.

I really hope you will consider posting some of those scripts. They would be really useful to me, and I am sure plenty of other people.

Frederiko

11

Spending “a lot of time on the software” rather than reading or creating is a real danger. Over the past few days I have been migrating my general-purpose journal and note card file and GTD-style project management center from Journler to DEVONthink (as I described in another post; see also the interesting blog post by Marko Wenzel on DEVONthink as a Zettelkasten Note Archive, although I intend to use DEVONthink, like I used Journler, as both a note card file and a GTD-style project management system). Over the past few days I have lost a lot of reading/creating time as I have worked to reconstruct my system in DEVONthink. But now that I am nearly finished with the migration, I expect that the system will require zero maintenance time so that I can focus completely on reading and creating (until a future migration to other software, if I live long enough).

I too use BibDesk for citations only, as Tom described, but I cite many references (I’ve accumulated over 20,000 in BibDesk over the past decade) so I have found that it adds a lot of value to my note card system if individual BibDesk entries (references) are listed in DEVONthink’s see-also list, which can be done fairly easily using the method I described in the thread titled How to index individual BibDesk entries in DEVONthink.

BibDesk can auto-file PDFs in a folder and you can easily index that folder in DEVONthink (although I don’t do this). Within BibDesk you can organize citations by keywords (tags), smart folders, or static folders. BibDesk has an ingenious template language that I’ve used to amazing effect over the years. There is no built-in support for Citation Style Language (CSL) but if you need to use CSL you can easily import your citations into Zotero (I’ve never needed to do this).

You can also link to individual BibDesk entries in any note (or anywhere else in Mac OS X) using BibDesk’s URL scheme (x-bdsk://citekey), or you can select a cite key in any text and use the Services menu item Show Reference With Cite Key that is automatically installed by BibDesk. Importantly for power users like me, BibDesk stores citations as BibTeX, a plain text format that can be very easily manipulated with grep or other batch processing tools.

1 Like
12

BOOKENDS, for many reasons. It’s fast, supported on a daily basis by unmatched response via forum. It works with iCloud now, and suits LaTeX well. It also manages smart folders like DT does, and it has a host of uselful features; one of which is a depth control tag cloud; plenty of organizational tools.

I use a system to classify sources by “AuthorYear - Title”. Bookends automatically renames any file I import to this format. Just use Biblio->Formats Manager to customize to desired form. The sources are fully indexed in DT. Because the indexed folder mirrors the Bookends attachment folder there is no pressing need to URL link the references between both programs.

The AuthorYear becomes the LaTeX key automatically generated by the software. Bookends. exports the contents of a static folder as a bib file for a LaTeX editor to compile the whole project.