Which reference management software should I use?

March 4, 2007 6:26 PM

Which reference management software package should I use?

What is basically the most common / de facto standard, if there is one? Is it helpful to use the standard, in terms of sharing resources? Or does it not matter so much?

What is the most useful / flexible / import-exportable? What is the most likely to not go bankrupt in 10 years after I've put in an irreproducible amount of work into building my database?

Which do you like best, and why? Which is the easiest to work with? Which integrates best with Word? Which integrates with (La)Tex/BibTex?

Is there anything else worth knowing?

(I'm on a PC, but often use Macs at work and school. I have access to EndNore, RefWorks, and of course the open source BibTex options, but am open to purchasing anything reasonably priced.)

posted by ChasFile to education (24 comments total)

For latex, I just started using bibdesk, which is pretty great (but mac only). It does a lot of things I've been looking for, including tagging (though there are some interface issues with doing more complicated things), and managing your pdf files for you. Also seems that it is being improved very actively. It uses a plain .bib file as its backend database, so even if the program just vanished tomorrow, the file would still be perfectly readable.
posted by advil at 7:01 PM on March 4, 2007

I bought EndNote and pretty much hate it. Though I have Endnote 9 and 10 might be better. It creates bibliographies that I have to edit, a word file that I have to edit and it's generally clunky and doesn't save much time for me at all. I've heard there are better ones that integrate with Latex.
posted by mulkey at 7:02 PM on March 4, 2007

If you want your library to be in a perpetually readable format, and you use LaTex, you should probably stick with BibTex. That said, people seem to like Endnote for integration with Word.

Web of Science and the other citation search indexes provide export to a number of formats, and the bibtools bundle from CTAN will convert ISI-formatted reference lists into a Bibtex-friendly shape.
posted by janell at 7:05 PM on March 4, 2007

Oh, and I forgot --- I like BibTex, and I use the keywords and comments field (with grep) for effective tagging.
posted by janell at 7:06 PM on March 4, 2007

I hate EndNote too. It's better than doing things manually, although as mulkey says, you still have to edit the results. And sometimes the much vaunted templates for every major journal don't even match the journal's style! I wouldn't consider using it to just store lists of references—too clunky.

If there's something that works better with Word, I'd love to know about it.
posted by grouse at 7:23 PM on March 4, 2007

Endnote is the way to go. I was a die hard Reference Manager fan and resisted shifting for a long time. I finally had to, simply because Thompson stopped development on the other two (the 3rd one being ProCite). They tell you this when you call and ask for advice.

Endnote has grown on me. It works great (especially cite while you write), easy to collaborate and everyone I work with has it.
posted by special-k at 7:29 PM on March 4, 2007

Depends on the subject: EndNote/RefWorks seem better suited to sciences, and suck at arts/humanities. Even with its shortcomings, BibTeX is more robust, portable and adapts better to different front-ends as long as you stick to the spec. (Bookends is a nice Mac app that's much more than a front-end.)
posted by holgate at 7:29 PM on March 4, 2007

I've had good luck with a Bibus/Open Office combo, though maybe not what you're looking for exactly.
posted by chrisamiller at 7:52 PM on March 4, 2007

Microsoft OneNote 2007.
I've used 2003 version... the 2007 version is much better.

If you get the teacher's edition Office2007... I think it comes with it..

I gotta feeling that this piece of software is going to be like the Word in few years.... Can't live with out ....

This is a solid and extreamly flexible app for any ref/note taker and researchers...
posted by curiousleo at 8:07 PM on March 4, 2007

I (work only on Macs and pretty much only in LaTeX and) use CiteULike and BibDesk.
posted by dmd at 8:11 PM on March 4, 2007

Depends on the subject: EndNote/RefWorks seem better suited to sciences, and suck at arts/humanities. Even with its shortcomings, BibTeX is more robust, portable and adapts better to different front-ends as long as you stick to the spec.

So which are well suited for the humanities and social sciences?

Which BibTex front ends would you recommend? I'm using JabRef now.

Does anyone have experience with Biblioscape? I've played with the trial some, but it doesn't seem to want to export into BibTex or any other universal intermediary file format. I do like that I can set up a server with it, though, which seems like a nice balance between the advantages of RefWorks (accessible anywhere, easy to share) and EndNote (local copy to maintain / back up, accessible offline). Thoughts/impressions?
posted by ChasFile at 8:15 PM on March 4, 2007

RefWorks is a disaster, at least for the humanitdies. You'd be shocked at the number of errors it produces. It's nice because you can access your citations from computer, but don't expect it to produce quality bibliographies. You will actually spend more time fixing errors in a RefWorks biblio. than it would take to compile one from scratch.

I have heard that EndNote is considerably better, but I haven't tried it out yet.
posted by HotPatatta at 8:20 PM on March 4, 2007

I'm in the biological sciences.

I use EndNote. I don't think it sucks. I do wish it worked with something other than Word (like OpenOffice), because at the moment it's the only thing tying me to Word.

I've tried getting into Bibtex, but I just couldn't get it to work. I couldn't find a frontend that was in any way decent - they all sucked compared to Endnote. However, I'm sure there's lots I haven't tried (I've never heard of the "JabRef" you mention, for instance). I also had trouble finding out how to find templates (or whatever you call them) to format the references as required. And I didn't even get around to figuring out how Bibtex interfaces with Word (so I can hit some defined key and have it insert the selected reference, like Endnote does). So, my efforts at Bibtex completely failed due to the high learning curve and lack of sensible information on how to use it in a practical way.

On top of this, my efforts to get into Latex in general were also hampered by my inability to understand, once again, how to install the templates or classes or whatever I wanted...and the fact that all the journals I look at publishing in now pretty much require submissions in Word format anyway.

*tex probably totally rules once you understand it, but at the moment, Endnote works for me.
posted by Jimbob at 8:24 PM on March 4, 2007

(Just installed JabRef by the way, and in terms of Bibtex front ends, it's the best I've seen. But I'm still looking for the "Send this Reference To Word" button, and the "Format References In This Document" function. I guess I'm just thinking in a different paradigm than Bibtex.)
posted by Jimbob at 8:36 PM on March 4, 2007

Another vote for Endnote here.

I am with Holgate though. Having worked in both science and the humanities I can safely say that Endnote is works a lot better in science.

If you bibliography just contains book chapters and papers from journals (such as in the sciences), accessible from Medline and Pubmed, - then it works a dream.

However humanities essays might cite a lot of different sources (books, film, interviews, documents as well as papers), this is where Endnote falls down as manually adding sources to your library is a pain in the ass.
posted by TheOtherGuy at 8:41 PM on March 4, 2007

wow curiousleo you're completely off-topic here. I like OneNote too (which has nothing to do with managing references btw) . It also has a zero chance of replacing Word because they serve completely different niches.
posted by special-k at 9:14 PM on March 4, 2007

Is it helpful to use the standard, in terms of sharing resources? Or does it not matter so much?

Use whatever you like best. Any time you save by importing someone else's cites from time to time will be more than swallowed up by the extra time it takes you to deal with a system you don't like.

What is the most useful / flexible / import-exportable?

Editing your bibliography.bib with a text editor and dumping the cites in manually.

What is the most likely to not go bankrupt in 10 years after I've put in an irreproducible amount of work into building my database?

Editing your bibliography.bib with a text editor and dumping the cites in manually.

Which do you like best, and why?

Editing your bibliography.bib with a text editor and dumping the cites in manually.

Why? Because I don't have to learn anything else. To input a new article, I grab the last article I see, copy it, and input the new stuff over the old stuff. Done, and I didn't have to learn new stuff to do it.

The way I work is:

(1) Write paper, ignoring that I might not have all the cites in my bibliography.bib.
(2) LaTeX, bibTeX.
(3) See what bibTeX bitched that it couldn't find.
(4) Input those, being very strict about the mnemonics -- always smithjoneswossname2002, or whatever. Step 4 takes about a minute.

Which is the easiest to work with?

Over the long run? Editing your bibliography.bib with a text editor and dumping the cites in manually.

Which integrates with (La)Tex/BibTex?

Editing your bibliography.bib with a text editor and dumping the cites in manually. At most, a TeX-aware editor that will dump a blank article or book entry for you.
posted by ROU_Xenophobe at 9:15 PM on March 4, 2007

So which are well suited for the humanities and social sciences?

I can only speak to the humanities, and say that there is no ideal reference/citation/quotation manager that fits the way a historian or classicist or literature student works: if there were, I would know about it, having spent a long time looking.

On the Mac, DevonThink, or Yojimbo to a lesser extent have good free-text and quote-storage elements, but lack when it comes to structured and formatted footnotes and bibliography entries.

Anecdotally, the social sciences vary: EndNote fits better with ones where research is based more upon citing journal articles than books (e.g. psychology and others using APA style), but not so much with disciplines where you're using books and other sources, and need to quote material.

If you need to know what page of a book a particular quote or passage appears, as opposed to the pages of a journal for an article, EndNote pretty much sucks. And although BibTeX was also created for cite-that-journal disciplines, it seems to have been adapted well with quote-that-book. I've used jurabib, which literally kept my doctoral thesis in check, and there's also biblatex, which is a newer reimplementation of BibTeX for historians.

I tried Biblioscape some years ago, and found it a pain; I was also migrating away from Windows at the time, though, so your mileage may vary. Some academics swear by Nota Bene's reference-management and document-preparation tools, but it was old and unwieldy when I tried it, and by the time the new versions came out, I'd moved my work environment over to Linux and then OS X.

Picking up on what JimBob said, the tools most tightly integrated with Word are most likely to tie you to Word and lock you into proprietary formats. This is, as you well appreciate, not always a positive thing.

Trying to avoid a derail, but as I always say in threads like this, if you're planning on writing dissertation-length works in Word, consider the alternatives. OpenDoc might change things, but a long document in Word is a nightmare waiting to happen, regardless of how many times you backup. It also means you worry less about Word-compatibility for ancillary tools.
posted by holgate at 9:24 PM on March 4, 2007 [1 favorite has favorites]

And on preview, picking up on ROU_X, all I've ever used seriously to manage .bib files has been Emacs's BibTex-mode. It appeals to my academic control-freakery.
posted by holgate at 9:26 PM on March 4, 2007

I'm one of those who swear by (and, as with all programs, sometimes swear at) Nota Bene, which is actually a suite of programs (see http://www.notabene.com/). The integral bibliographical manager is called Ibidem, and there's a new component called Archiva that enables one to automatically put information into Ibidem when searching.

A very promising, and free, tool that you really must look at is Zotero, developed by the Center for History and New Media at George Mason University (http://www.zotero.org/). You'll need Firefox 2.0 to run it.

Another program worth considering is Scholar's Aid (http://scholarsaid.com/).
posted by davemack at 3:31 AM on March 5, 2007 [1 favorite has favorites]

Picking up Holgate's comment about dissertation-length work using Word, I'd implore you -- for the sake of your sanity -- to do two things.

1. Use the 'thesis' template that's available in Microsoft's template library, so that you can maintain a consistent style. (See http://office.microsoft.com/en-us/templates/CT101172711033.aspx)

2. Break your work into separate files for each chapter.
posted by davemack at 3:42 AM on March 5, 2007 [1 favorite has favorites]

I will nth the recommendation of BibTex with the JabRef frontend.

I wrote my thesis in Lyx (on linux) and found cites to be easy to include.

Luck!
posted by achmorrison at 5:28 AM on March 5, 2007

I can't begin to imagine editing BibTex manually. That's why I love CiteULike.
posted by dmd at 7:41 AM on March 5, 2007

While BibTeX (and hence LaTeX) aren't the most user-freindly of experiences, they are robust, flexible and up to the demands of academia typesetting. I second the thumbs-up for BibDesk, and add a recommendation for c2bib. This handy bit of software allows you to highlight and copy references from webpages, PDFs etc and then massages them into the correct format before pushing them into your .bib file. Truly a lifesaver.
posted by outlier at 9:20 AM on March 5, 2007