Biology Computers and social media Science

Searching the scientific literature through the years

After my experience with using (or, as at least one of my readers has suggested, misusing) my blog to get an article to which my university does not provide online access, it occurred to me just how much our means of accessing the scientific literature has changed in the last decade and just how radical those changes have been. Again, those who are old farts with me may remember that a little more than 10 years ago at the institution where I did my residency, we could do electronic searches of the Medline database, but it wasn’t over the Internet. Basically, the library bought access to Silver Platter, which contained the entire Medline database on four CDs. We would then go to the library to search those CDs and would either print out the text results or copy a text file with our search results to a floppy disk. In fact, back then, that’s also how we searched the Genbank database as well for DNA sequences. All these online tools for searching the biomedical literature or the Genbank database didn’t exist just a mere decade ago. Indeed, I remember in the early 1990’s, when I was a graduate student, when we bought MacVector (software for analyzing DNA sequences), we also bought a license for access to the Genbank database for one year. Every three months, the lab would receive a set of CDs containing the entire Genbank database, and that’s as often as it was updated. Heck, to do BLAST nucleotide alignments, we used to have to use an e-mail-based system, where we would e-mail the sequence of interest to the BLAST server, which would then e-mail back the search results.

Pretty primitive, eh?

But that’s not all. If you go back just a few years further, to the late 1980s, even that didn’t exist. Instead, to find articles that I wanted, I’d have to go to the Index Medicus, plow through big stacks of books containing these indices, write down the results, and then go to the stacks to find the journals containing the desired articles. We’d then have to photocopy those articles.

Thinking back on that, I’m amazed at how easy we have it now. All anyone anywhere in the world needs is an Internet connection to search PubMed, which now contains links right to many of the journals and the articles, right from the search results. If your university has purchased online access to the journal in question, you can simply download the article as a PDF right there (if it’s not so old that the journal hasn’t put it online). Even if your university hasn’t purchased online access, you can still read the abstract, which is often enough to determine whether the article is even of sufficient interest to seek out. If you want to seek it out, you can often e-mail the author to ask for a PDF of the article or manuscript or e-mail colleagues at other institutions that might have access to the journal. If you use a bibliographic database program like EndNote, you can even search PubMed directly from within the program, download any citations you like, and then use the software to put the citations directly in any manuscripts and grant applications you may be writing. It’s truly amazing.

Man, I feel old. Next, I’ll be ranting, “You punks don’t know just how easy you have it! Back in my day….”

By Orac

Orac is the nom de blog of a humble surgeon/scientist who has an ego just big enough to delude himself that someone, somewhere might actually give a rodent's posterior about his copious verbal meanderings, but just barely small enough to admit to himself that few probably will. That surgeon is otherwise known as David Gorski.

That this particular surgeon has chosen his nom de blog based on a rather cranky and arrogant computer shaped like a clear box of blinking lights that he originally encountered when he became a fan of a 35 year old British SF television show whose special effects were renowned for their BBC/Doctor Who-style low budget look, but whose stories nonetheless resulted in some of the best, most innovative science fiction ever televised, should tell you nearly all that you need to know about Orac. (That, and the length of the preceding sentence.)

DISCLAIMER:: The various written meanderings here are the opinions of Orac and Orac alone, written on his own time. They should never be construed as representing the opinions of any other person or entity, especially Orac's cancer center, department of surgery, medical school, or university. Also note that Orac is nonpartisan; he is more than willing to criticize the statements of anyone, regardless of of political leanings, if that anyone advocates pseudoscience or quackery. Finally, medical commentary is not to be construed in any way as medical advice.

To contact Orac: [email protected]

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