This time, the title refers not to blogs (where I haven’t figured out the answer yet) but to scholarly articles.
Like most scientists I know, I tend to read journals online, accessing their webpages with a browser (usually Mozilla Firefox), reading either the HTML or the PDF on my screen, and only rarely bothering to take a printout. Many trees have probably been saved this way.
Also, like most scientists I know, when writing papers I use bibliography software (in my case BibTeX; Microsoft Word users are likely to use Endnote) to organise my references, and I maintain a database of papers I refer to.
The question is, what happens in between? There are two problems here: I want to save my reading material in a systematic way, so that I will find it again when I want to; and I want to save the citation information for it so that I can easily reference it in my own writing.
Saving things systematically is not my strong point. Ideally, I would save it to a subdirectory named after the topic of interest, and rename the file with an informative name, so that I can locate it with a simple directory listing. If a file belonged to multiple topics, I would make symbolic links to it in all relevant subdirectories. I’m sure it would work well. Instead, what I end up doing is saving everything to a directory named “papers” (or, worse, on my desktop), with the original filename which could be something like “10.1371_journal.pcbi.0020053-L.pdf”. Good luck finding that again. Then when I need it again, I end up searching PubMed or Google Scholar for it.
As for citations, an alternative to the extreme tedium of manually entering each BibTeX entry into my database was to search for the paper on sites such as Hubmed (a PubMed front-end that can export to BibTeX format and do other nice things). This, in practice, is not tedium-free either.
Such was my workflow until recently. Now I have a better solution: Zotero.
I’m sure I’m late to the party and lots of people are using it already, but here’s a description for the uninitiated. Zotero is a Firefox extension: when installed, you get a “zotero” button at the bottom right of the Firefox window, which when pressed, pops up the Zotero interface (or pops it down again). What it does is, it captures bibliographic information about the page you are currently viewing, and saves it to a database. Capturing is as easy as clicking an icon that shows up in your URL bar. (It’s not restricted to scholarly journals: it works with news articles from the New York Times, or BBC News, for example.) Each item in that database has numerous fields: the usual bibliographic ones (title, author, journal name, etc), but also web links, notes, attachments, tags. It automatically extracts tags from some articles (via their “keywords” or equivalent section), but you can specify your own. You can search your articles, filter them by tag, and do various other neat things, most of which I haven’t explored. Most importantly, you can export citations in BibTeX format (and also Endnote and various other formats).
Zotero works with Firefox 2, and the latest version also works well, in my experience, with Firefox 3 RC1, but has glitches with the previous release (beta 5) of Firefox 3. If you are overwhelmed by scholarly reading matter, give it a try.