If there is a single basic irreplaceable tool for research in the life sciences, it is surely PubMed, the literature database of the US National Library of Medicine. PubMed is irreplaceable not just for scientists but for anyone with a professional (or even personal) interest in life science research.
That very much includes science writers, for whom PubMed is essential. And deeply beloved. I speak as one who did it the hard way before there was PubMed, spending hours and days in the stacks of difficult-to-access medical libraries, taking notes on 3 x 5 index cards. Looking back, I don’t know how I had time to get anything written at all. PubMed changed my world, very much for the better.
The heart of PubMed is its collection of bibliographic information and abstracts from nearly every journal in the world that touches on the life sciences, which means not just Science and Nature and JAMA and NEJM, but also journals in related fields like anthropology and paleontology and computers and economics and even astronomy and physics. Find the journal list here.
How to get full texts of journal articles
Many years ago I took a science writers tour of NLM and asked the then-director if there was any hope of full texts of journal articles online. He put on a long face and said he didn’t see how it could happen, what with copyright and journals being money-making operations.
That was then. It’s a new world. Some funders now require grantees to deposit their journal articles in PubMed, and even commercial publishers make articles open access on occasion. Full text is increasingly available, and when that’s the case, the PubMed reference includes a link to the complete paper. Here’s PubMed’s tips on how to get full texts.
PubMed goes way beyond journals
Journals are the heart of PubMed, but there are other riches to be had there too. Here are just a couple of examples; there are many more.
Some PubMed services are of use chiefly to scientists, like access to the human and mouse genome sequences. But writers find treasure there too, such as the directory of human genes and disorders known as OMIM, Online Mendelian Inheritance in Man. Find the many genome resources here.
For some reason it is not widely known that PubMed also provides full-text access to hundreds of textbooks and reports. Start here.
And PubMed is all free, a matchless gift from the American taxpayer.
PubMed Commons: Changing peer review forever, and improving science while it’s at it?
I am telling you all this in case you don’t already know about PubMed. And even if you do, you may not know that PubMed has just launched PubMed Commons, a system for commenting on journal abstracts. It’s an experiment that “could change the process of peer assessment of scientific articles forever.” So says James Coyne at Mind the Brain.
Coyne takes an entirely rosy view of PubMed Commons. It might, he says, be “truly revolutionary. PubMed Commons is effectively taking post-publication peer review out of the hands of editors and putting control firmly in the hands of the consumers of the scientific literature—where it belongs.” His is a long explanatory post, with plenty of criticism of letters-to-the-editor as a vehicle for what evolutionary biologist Michael Eisen calls post-publication peer review.
Eisen, a co-founder of the open-access Public Library of Science, where you’re at right now, has long advocated for post-publication peer review. But the efforts so far, he explains at It is NOT Junk, are either awkward to use or haven’t caught on. Eisen describes himself as excited and cautiously optimistic about PubMed Commons. “The obvious place to build such a commenting/post publication review system has always been directly in PubMed – it has everything and everyone already uses it.” He urges scientists to join up and join in, helping to make the new system work by committing to comment on a paper at least once a week.
Drug Monkey thinks PubMed is just the right place for post-publication review too, and also urges scientists to sign up and contribute to PubMed Commons. He says, “I will be eager to see if there is any adoption of commenting, to see the type of comments that are offered and to assess whether certain kinds of papers get more commentary than do others. All and all this is going to be a neat little experiment for the conduct-of-science geeks to observe.”
I guess I’m one of those conduct-of-science geeks (although I think of myself as more of a nerd than a geek.) And, as it turns out, I can probably qualify to check out the commenting action. And comment myself.
That’s because, although PubMed Commons is a private system for now, many science writers are probably eligible to join. You only have to be an author on any publication in PubMed (even letters-to-the-editor) and then get a registered participant to sign off on you.
It was my impression these membership restrictions apply only to this initial test period, but Ivan Oransky seems to think not. He has a post at Retraction Watch complaining about confining participation to scientists only. The PubMed net is actually wider than he implies; it includes more than just certified scientists. I’d never thought to do a PubMed vanity search before now, but it turns out–to my surprise–that dozens of my publications are listed. Ivan is in there too. So we both qualify–and so, I bet, do a lot of our peers.
Ivan is also unhappy about the exclusion of anonymous comments from PubMed Commons. His post includes ruminations from several of those involved in setting up the new system. They describe internal arguments over whose critiques should be allowed. Dozens of comments follow his post (and a good many, of course, are anonymous.)
Ivan’s quotes from National Library of Medicine director David Lipman suggest to me that the PubMed Commons membership restrictions are not engraved in tablets of stone. PubMed Commons is, after all, in the very earliest experimental stage, which means it will evolve.
At the British Medical Journal Group Blogs, BMJ deputy editor Trish Groves is worried that PubMed Commons will worsen what she thinks is PubMed’s already strong (negative) impact on the future of journals. She points out that the BMJ Rapid Response system has published nearly 100,000 comments about its papers, and they’ve been doing it since 1998. PubMed Commons, she suggests, can discourage journals from doing the right thing in providing for critiques on their own sites.
Maybe she’s right. It’s not good to damage the journal ecosystem unnecessarily, especially excellent journals that are open-access, such as BMJ. Still, the excellent open-access PLOS journals (where On Science Blogs now lives) don’t seem worried. As PLOS co-founder Michael Eisen notes, it’s undeniably efficient and convenient and simple to consolidate post-publication peer review in a single place, one that, like PubMed, people visit all the time anyway.
The first priority needs to be to encourage post-publication peer review and to raise its profile, as PubMed Commons will try to do. Post-pub review is not just navel-gazing or a way to provide disgruntled researchers with a place to vent. It’s one crucial long-term step toward combing the crap out of the scientific literature and making it more trustworthy.
We need more marijuana genome projects
It’s part of blogging culture to self-promote. And since I’ve written about marijuana twice so far here at On Science Blogs, it seems only right to direct you to my most recent disquisition on pot. This one is a blog post about the Cannabis genome, which appeared over at the Genetic Literacy Project.
A tidbit I discovered in researching this piece: while there are a zillion genetically different strains of cannabis, they are all the product of conventional breeding techniques, some of which have been around for thousands of years. Attempts at genetic modification–21st century laboratory techniques for manipulation of single genes–have so far failed. So no worries that what you’re smoking (for medical reasons, of course) is GM pot.