Tag Archives: Bibliography management

Installing Gerd Neu­ge­bauer’s Bibtool on OS X

I struggled for more hours than I would like to say trying to compile Gerd Neugebauer’s BibTool utility on my mac (OS 10.9.2). I kept running into problems with the kpathsea libraries. Not surprisingly, an old thread on the Mac OS-TeX mailing list provided the necessary insight. I’m reposting it here so that it might get better exposure on the Internet for those trying to do the same thing. Of course, someone who wasn’t shamelessly hacking away at it probably wouldn’t have had any problem at all . . .

BibTool is an amazing utility that does all those things we all wished BibDesk would do, but doesn’t: command line tools for removing fields, rewriting fields, grabbing references based on various criteria including regular expressions, pretty printing.

On Nov 23, 2009, at 1:49 PM, Jan Erik Moström wrote:

> I’m a bit slow (in all kind of ways 😉 and I’m just trying to figure out the MacTeX distribution … one thing that that I would like to do is to install “bibtool” (not bibtools) but I can’t figure out how to do this in a simple way. Using Gerbens TeX distribution it was possible to use the i-installer but now I’m at a loss how to do it.

You can download the source and compile it yourself from http://www.ctan.org/tex-archive/biblio/bibtex/utils/bibtool/
(Get the *.gz) file.
Once you have expanded the tar archive, copy the makefile.unx file to makefile, then run
sudo make install
sudo make install.man
This will place a working copy and manual pages in the /usr/local tree.
As long as you have /usr/local/bin in your path, things should work.

Of course, you have to have the developer tools to do this.
There are many options to set specific details during the compilation process, but I just did a vanilla “make” and
./bibtool -h
gave me the typical “usage” statement.

I’ve never used bibtool, don’t know how to use it, and don’t have any test files to ensure that it works in a real-life situation.
Otherwise, I now have a seemingly-functional version of “bibtool” that runs on X86_64 Snow Leopard.
I don’t guess that really helps you, but if you want it, send me a message off-list.

Files for Pratt LIS 663

Tonight I am guest lecturing at Pratt Institute School of Information and Library Science. The topic is ontology. This post is mainly for the students; they will be able to find the lecture notes and the “Make your own ontology” worksheet here.

The worksheet is HERE.

The lecture notes are HERE.

“Avalanche control” in scientific literature: A role for informatics

In “We Must Stop the Avalanche of Low-Quality Research,” it is claimed that much of the scientific research literature published recently is “redundant, inconsequential, and outright poor” and that “research has swelled in recent decades, filling countless pages in journals and monographs.” “Countless” is intended in a negative sense here. No argument is provided for the first claim, unless the claims about frequency of citation—generally very low, if at all, for any paper in the literature—are to be taken as an argument that recent literature is poor in quality. It does seem clear that the authors believe that there is too much literature, and it seems to me that their claims and arguments that there is too much literature might be just as strong if it weren’t paired with the argument that the literature is generally low in quality.

Taking a larger view, the problem is probably worse than the “Avalanche” authors suggest. A prominent case in point: the Biodiversity Heritage Library, whose holdings amount at present to 30,512,292 pages in 80,976 volumes, is growing daily, and more and more libraries are joining the project, including those in Europe and the Pacific rim. (Perhaps the “Avalanche” authors would find this reassuring. Back in the good old days, when men were real men (and women didn’t do science), only what was worth reading was published, and everyone read it.) Nonetheless, finding works relevant to a given topic is difficult and will become more so.

Continue reading