Citation Managers For Unix?

A studious Anonymous Coward asks: "So, I now mostly converted to Linux, however one key applications that is missing: a tool like 'EndNote' or 'Reference Manager', which is invaluable for collecting and managing bibilgraphic resources when doing scientific research and writting scientific papers. These packages will do things like maintain a searchable database of your references which you can populate off of one of the public citation databases (pubmed, etc.). Additionally, it interoperates with Word to format your bibliography and (re)number your references. Is there anything like this for Unix?"

Comments

Standard is bibtex.

[Anonymous Coward]

If you are writing academic papers, you will probably end up using latex and bibtex at some point. Bibtex is the standard tool for handling bibliographies, but personally I think it sucks. There are quite a few tools around for handling bib files, searching/sorting/formatting. You'll find it a god awful pain in the ass compared to EndNote though. I've used EndNote, sobbed at what I was missing out on, then went back to my unix (not linux;-) box. Won't someone with more time on their hands port/hack something like EndNote for unix please?

Re:Standard is bibtex.

[e271828]

I've been searching for the right tool for quite a while now, but am yet to find it. We use latex/bibtex for all our papers, so I need to keep my refs in bibtex format. For now, I just use Emacs' bibtex mode, which functions quite nicely for entering biblio information. Fancier GUIs are available: for instance, take a look at the cross-platform TkBibTeX.

You can also "roll your own" using the perl modules from btOOL.

My general dissatisfaction with the freely available tools means that a bibliography manager will be one of my first programming projects when I lay my hands on an OS X box in a few weeks (drool...)

Re:Standard is bibtex.

[e271828]

The use of LaTeX vs. Word is very much a field dependent thing. In the Systems area of Electrical Engineering (Communications/Controls/Signal Processing), LaTeX is used almost exclusively. On the other hand, the use of Word is quite common among EEs in the semiconductor area. I suspect that much depends on how "math heavy" your papers are. Interesting aside: to go with the above, conference presentations in the Comm field are almost always made using good old fashioned transparencies made using LaTeX, whereas semiconductor folk often use PowerPoint.

Disclaimer: I can speak with some authority regarding Comm., but the semiconductor obervations above are based on limited experience.

Re:Standard is bibtex.

[irony nazi]

I found bibtex to be a pain to use as well. I ended up keeping a huge alphabetized file of citations and I would either cut and paste the ones that I was referencing or I would remove the ones that I wasn't and include the file in my LaTeX documents.

Finally, I don't think that very many academic papers are written using LaTeX. I love LaTeX; it is both efficient and easy to use (once you learn it). Many mathematics and Physics journals use it, but all of the Engineering Journals that I've read the req.s for only accept MS Word or text files. Just so you know that I'm not BSing you, some specific examples are: J. of Amer Ceram Soc, Mat Res Bulletin, J. of Materials Science, Jap. J. of Ceramics.

It's funny, now you know what field my research was in.

Re:Standard is bibtex.

[grammar nazi]

Aagggh...
...you said 'OS X'....

(wipes drool)... Aaagh.

I too, plan on purchasing an Apple Powerbook as well as a fresh clean spanking new copy of OS X!

I can't wait you know. I really can't wait.

Re:Standard is bibtex.

[BozoE]

I used BibTeX/LaTeX to write my PhD thesis in a scientific field, with the Xemacs package to manage my entries. My wife wrote her PhD thesis in literature using EndNote/WordPerfect.

For some purposes, BibTeX is certainly is adequate. However, even if you are just adding and searching entries, it is closer to programming than to a user-friendly application. Here are just a few of the problems for a computer-non-expert: the changes to capitalization it does automatically (what, I need to say '{A}merica' to not get 'america'?), the funny-looking ways to enter accents, and the difficulty to debug if an entry is in the wrong format. Then, just imagine a non-progammer trying to change a citation format slightly.... Likewise, to most non-programmers, LaTeX looks like a step back to the dark ages, and since BibTeX requires the use of LaTeX, it's awfully hard to convince humanities scholars to use it. And of course, the journals would have no idea how to handle LaTeX code.

EndNote is our primary example of why we still mostly use Windows instead of Linux. I would love to see Niles port EndNote or to have someone else develop a product as easy to use.

Re:Standard is bibtex.

[woggo]

One very nice thing about BibTeX is that you can get BibTeX citations for papers directly from the ACM Digital Library (sometimes), from DBLP, or from Citeseer -- so you download the paper, view it, and if you like it, cite it! There are also many large repositories of BibTeX entries for all manner of papers available, especially in the DB and OO communities -- just do a google search for "inproceedings" and a favorite author if you don't believe me. :-)

Re:Standard is bibtex.

[blakestah]

Here are just a few of the problems for a computer-non-expert: the changes to capitalization it does automatically (what, I need to say '{A}merica' to not get 'america'?),

So this requires a bibliography style file change.

the difficulty to debug if an entry is in the wrong format

This is pretty easy for me. Since my Perl script adds entries direcrtly from Melvyl, a problem with an entry results in hacking the script, and that particular problem never arises again.

This is happening increasingly as people create GNOME and KDE GUI interfaces for searching and adding to the bibliography database files. The GUI interface does most of the work in formatting the entries and error checking.

And of course, the journals would have no idea how to handle LaTeX code.

Journal are idiotic in that sense. It is actually MUCH MUCH easier for them to print something already in a well described typesetting language, than it is to print something in DOC format.

EndNote is our primary example of why we still mostly use Windows instead of Linux. I would love to see Niles port EndNote or to have someone else develop a product as easy to use.

I've asked them to port to linux several times. First was about 5 years ago. They said they had no demand for such a product. Last year they said they were working on it, but they were more than a little perturbed by the lack of standardization in software for word processing. I mean, they didn't know if they should write for StarOffice, WordPerfect, Applix, Koffice, or FrameMaker.

I, however, will continue to use LaTeX. I have a few very simple reasons. The first is that the format doesn't change in ways that cause incompatibility every few years to lock in the customer base. I know with confidence I will always be able to read and print my files. TeX has been reasonably standard for over 20 years now, since before Bill Gates was writing a BASIC interpreter for QDOS. The third reason is that my bibliography database management can be done in the UNIX way. I have small files and programs that each do their own small job well. The fourth reason is that I can load the word processor on as many machines as I like for free. The fifth reason is that if something is broken, I can fix it. The sixth reason is that if I am armed only with a text editor, I can edit my files.

Now, not all these reasons apply to other word processors, but taken on the whole I think I will be using LaTeX for a long time.

Re:Standard is bibtex.

[blakestah]

BibTeX is just fine.

I have a Perl script set up to grab all email from Medline and automatically strip out the citations, format them, and add them to my database file. Even spent some time hacking bst files - now THAT is a weird language.

Anyone interested in the Perl script can email me. It won't work "out of the box" unless the email comes from Melvyl ie: the UC system. However, the principle is pretty similar for Medline and Melvyl emails. I just prefer the console Melvyl interface :)

Re:Wrong culture

[Matthew Weigel]

Unfortunately, I spent my last mod point on some yahoo who didn't read a linked article... I wish I'd saved it for this.

Some suggestions

[JDisk]

The author of this article(in german) compared some of the available tools with the Windows program "Reference Manager". His conclusion: There are no absolutely recommendable programs, but Sixpack, Pybliographer (and XEmacs in the bibtex mode) are strong candidates.

Wrong culture

[rjamestaylor]

The Unix culture (esp. the Free and Open parts) have little to no need for citiation management since this community disdains Intellectual Property, itself.

[Just kidding...]

Re:Wrong culture

[rjamestaylor]

Good point. The idea of hypertext (and, derivatively [sp?], HTML's tag) seems to facilitate this idea of knowledge chain.

Re:Wrong culture

[Cardinal Biggles]

Even though you're joking, you raise a serious point. This is actually a pretty common misunderstanding many people have about those who oppose intellectual monopolies.

I am personally opposed to copyright as a concept. But that doesn't mean I want to legalize plagiarism! People should be able to freely copy artistic and scientific works, but it should still be illegal to pretend that somebody else's work is your own.

I can't tell you how many times people assume that since you are opposing the right to monopolize certain ideas (or certain expressions), you are thereby automatically in favour of the freedom to falsely claim authorship of intellectual works.

OT: funny, not Troll

[irony nazi]

The above comment isn't a Troll comment, I find it rather funny. There is much irony in what it says. We all know that it isn't true, but it is indeed funny.

Since I'm the irony nazi, I guess that it would be my authority to point this out.

Please moderate the above to 'Funny'.

Use (X)Emacs and appropriate modes!

[Lars Arvestad]

When it comes to collection of citations, I believe you are basically out of luck if you rely on PubMed as your primary source. As others have pointed out, the situation is quite different in CS, math, and other (typically formula-heavy) fields. I have actually considered making a PubMed front-end that searches their database for you (they provide URLs delivering the result as XML) and then reformat for BibTex. Who is interested?

Regarding management of citations however, I don't believe you can get anything better than using (X)Emacs in conjunction with the right modes. For managing your citation file(s), you have the BibTeX mode which is marvellously simple. For writing your paper, you use AUCTeX mode and the RefTeX minor mode. With RefTeX, you can search the citation database without leaving your emacs session and choose among matching citations to get the one you want in at the point. There is also support for managing references to figures and tables. For example, you can list all labels (to equations, figures, and tables) in a buffer, indented after sectioning.

But the inquirer confuses me regarding one thing. It is listed as a feature that EndNote can renumber your citations. In Latex, who cares?! You get all those details for free.

Lars
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