Sometimes you come across a program that fulfills a need that you never knew you had and gratifies it in an immediately satisfying way. Zotero is one such program. It is a Firefox plug-in that allows you to store references to journal articles and books with a sweet click on a Zotero icon. Everything is stored in your browser. I never knew that collecting citations could be that easy.

But I wouldn't have heard about it if were not for Thomson Reuters, the publishers of Endnote and the Web of Science, litigating against this open-source program. What? Litigating against a free program? Actually you can't really sue an open-source piece of software, so they've resorted to suing George Mason University.

This is really nothing but the panic caused by the same corrosive technology change that has wrought havoc on the music publishing industry and newspaper clasifieds. As the internet sticks its fingers into more information sources, the real value that used to be leveraged in gathering the citations of the worlds journals has evaporated. The money jar is drying up and any aspiring middle level executives in these international conglomerates would be wise to panic. And as anyone who is familiar with RIAA, frivolous lawsuits is the only weapon these executives have.

The irony is of course that the story of the litigation on reddit was the piece of marketing that brought my attention to Zotero. And as I was in the midst of chasing references for my latest manuscript, I was in just the right place to put it through its paces.

As Paul Graham once said that Google succeeds because its business models runs with the grain of the internet. In such a way, Zotero runs in the grain of how I (and presumably other younger scientists) actually do reference searches. We do everything in the browser.

Typically, I would find everything first in the browser, then carefully type keywords in Endnotes to find the same article reference again to put it in my citation database. The genius of Zotero is to cut out a completely redundant step by putting the citation database in the browser itself, and letting you click on a icon.

But not only is the work-flow of Zotero vastly superior, it has made a canny assumption about how to manage the world's database of article references. Namely, it doesn't. Whereas Endnotes must access the API of a carefully curated database of citations such as Web of Science, or Pubmed, Zotero has taken a bottom-up approach to this problem. Instead of curating a database which you must access, it just has a library of screen-scrapers for as many journal websites and search websites as it can find people to write them. The heart of the system is a bunch of regular expressions and html queries. What smarter way to do it all in javascript as a plugin in the browser? Genius.

Think about the way that most of us find articles is to search for them in Google, or read complete articles. Then we gather the references. The need to go to a third-party database of citations is almost redundant. Actually with the existence of Google Scholar, it's actually redundant. And the search in Google Scholar kicks the ass of Web of Science. You can almost hear the hiss of air deflating out of the lucrative academic market.

Indeed, by leveraging the webpages as the source of the citations itself, Zotero is banking on the future – all the world's scientific literature will eventually end up online. Even the Royal Society has in the last year digitized their entire archives dating from the 18th century. With governments starting to mandate open-access, I can only see that eventually all publishers will be forced to comply.

Given the freely available .pdfs and article texts on the website, Zotero's well thought out annotations means that I can dispense with my article pdf libraries. I just need my Zotero database, and the automatic built links to the actual web-page of the article. Sorry Papers.app, you were good to me once.

It amazes me to see the improvement of citation software over the years. I still remember the pain of manually organizing the references to my thesis almost 9 years ago, in Microsoft Word. Changing the journal format was one of the most tedious activities in the world. Discovering Endnote was a revelation in managing references in Word. One click and the journal format magically changed before my eyes. Then I discovered the Web of Science, which eliminated hours in the library. The increased availability of .pdf's and laser printers meant that I didn't need to stain my hands with photocopying inks. And with Zotero, I can do all this in a browser. You tell the kids these days and they won't believe you.