In a recent announcement, GMU reports that they will be dropping their Endnote license:

With litigation pending between Thomson and Mason, we’re letting our campus site license for EndNote expire at the end of November. When it lapses, any copy of EndNote that was downloaded and installed under the terms of that license will have to be uninstalled and removed.

In addition, GMU has provided a helpful website explaining how to migrate from Endnote to Zotero.

This disturbing incident is further evidence, if evidence were needed, of the perils of keeping your data in propriety formats. Keeping your data in formats that comply with open standards is really the only guaranteed way to control and reliably share your data.

Update Kieran posts about it here.

One useful thing that academics share, though less often than their research, is their bibliographies. LaTeX is predominant in academia, though not universally so. So many of these online bibliographies are BibTeX files. See Benj Hellie’s BibTeX file as an example.

Sometimes, these have been converted to HTML. Sometimes, as in Benj’s case, the author simply posts the text file (BibTeX is a flat file database kept in plain text). This has some limitations. One problem is that the author has to periodically export to HTML, and even if he is posting the text file, it still needs to be uploaded to the server. Unlikely that this is done after each change to the bibliography.

From the users side, there are problems too. Suppose I have downloaded Benj’s BibTeX file. Some time passes, and I want to take advantage of Benj’s hard work. Some of the entries I already have, some are new. Some of the new entries may overlap with entries that I have made independently. Manually merging this material can be a pain, even with diff tools.

All of this would be a lot easier if academics used distributed version control to share their bibliographies. Suppose the distributed version control system in question is Git. When an author makes a change to his bibliography, then all he need do is to commit the change and push to the remote repository:

$ git commit mybibtexfile.bib
$ git push

From the users side, to download the bibliography all he need do is clone the git repository:

$ git clone git@github.com:PhilGeek/bib.git

After that, fetching and merging new changes is easy as:

$ git pull

Well, I am putting my money where my mouth is and publishing my BibTeX file in an open Git repository hosted at GitHub—http://github.com/PhilGeek/bib/tree/master. To clone this repository:

$ git clone git@github.com:PhilGeek/bib.git

Even if you are not a Git user and are shy about adopting new technology, the file can be viewed and downloaded here.

There is not as much in it as there should be. Before becoming a plain text Geek, I kept my bibliography in EndNote. Unfortunately, my EndNote file, a proprietary binary format, became corrupted before I could convert it to BibTeX. Yet another cautionary tale speaking in favor of the Power of Plain Text.

Consider direct quotation—no easy phenomena. Part of the point of citation, here, is so that the reader can read the quotation in context, to decide for themselves whether the quoted author has been misrepresented. The usual case is to quote from a dead tree source—a printed book or journal. Imagine if books were quite different than from the way they actually are. Suppose that every time a book is closed the text would change, sometimes subtlely, sometimes less so. When your intrepid reader tracks down your citation, the quote may or may not be there. What would be the point? There would be very little, if any, point at all. The requisite stability would be missing from texts that spontaneously morph.

One good thing about dead tree sources is that they don’t change in this way. But now consider delivering text online. It is easy to change HTML or upload a new version of a PDF. The nature of the medium does not guarantee the stability guaranteed by ink on a page. Instead of natural law, we have the moral law. We must rely—God help us—on trust. This is manifest in bloggers’ convention of striking through changed text in a post. Leaving a trace of a misspelled word, a hasty judgment, or mal mot is a sign of good faith, and bloggers who depart from this convention are subject to (verbal) sanction in comments or in pingback posts.

As the delivery of academic journals is moving increasingly online, editors face a corresponding moral challenge. The Aristotelian Society publishes papers online before the print volume hits the stands. Once an author asked to change his article after the online version went live but before the print volume was typeset. What was the problem? Things change online all the time!—he implored. The problem was simple. It would violate a precondition for the possibility of citation.