Archive for the 'PubMed' category


Mar 16 2011 Published by under Publishing, PubMed

I was talking to a grad student about publications and access to articles a while back and thought that I should write a little primer on it for other noobs to read. So I think somewhere somehow sometime someone listed the stat that NIH funded projects generate nearly 80,000 articles per year. And since the government is coughing up the money for us to do the work, in the spirit of transparency, these articles and the results and conclusions contained in them should be made available to the public.

And since Joe and Josephine Six Pack can’t really afford access to medical journals, researchers, whose research is funded by the NIH, are required to post articles in the PubMedCentral (PMC) library within 12 months of publication. The requirement is limited to peer-reviewed articles, and doesn’t include book chapters or conference proceedings, etc. I believe these requirements kicked in for anyone receiving direct funding from the NIH starting FY 2008, so don’t go grieving some PI about stuff they published back in ’68. Why are we doing this?
-Well first off, you are letting your investors, the taxpayers, see what we are up to.
-Next you are putting your science out there and hopefully making a name for yourself.
-Pumping up your citation stats
-Prepping yourself for future Open Access regulations that are starting to take root in other agencies such as the NSF.
-So Nana who lives in East Jesunuckistan can see your latest article when she fires up her Prodigy account on her 14.4 kb/s dial up account.

And for you noobs, PubMedCentral ≠ PubMed. PubMed holds citations for more than just journal articles dating back to around post-WWII, it also includes links to PMC in it. Also PMCID is not the same as PMID, but if you have one and need to get to the other, here is the converter. And sometimes you will have to wait since articles don’t always get a PMCID number right away and you are just stuck with the temporary NIHMSID.

So how do you make sure your stuff ends up in PMC? Great question, there are generally four typical routes that this happens.

1. Publish in a journal that deposits all final published articles in PMC that don’t require any action on the author’s part. This is the easiest option of all and here is a list of journals that will do it for you.
2. Make arrangements to have publisher deposit final published article into PMC.
3. You deposit the peer-reviewed manuscript via the NIH Manuscript Submission (NIHMS) process. This differs from the previous two options in that those options use the journal’s final article and this option publishes the article in the manuscript format, so it’s not as pretty.
4. Some publishers will kick start the submission process in NIHMS but you have to finish it. They’ll dump the article in the hopper but you have to give it the thumbs up.
A lesser-known option is that you can pay me to do it for you. Yeah it will cost you a little more, but when your article’s PDF pops up on PMC with actual liquor stains on it, you’ll feel mighty proud.

7 responses so far

Casting your net...

Mar 14 2011 Published by under Grad School, PubMed

So I think one of the smartest things that I did as a grad student was to create an NCBI account so that I could schedule in saved weekly searches of the PubMed database.  That way I don't miss the pertinent literature or have to go lurking for it, it comes straight to me.  For instance, lets say you study Rump Shakin, why not follow the big whig Rump Shaka of your field, that way you can see that groovy person's new papers to determine if they are pushing the field more towards the Humpty Dance or are they skewing towards Poppin & Lockin.  There are endless possibilities of searches to set up and can come to you, daily, weekly, monthly, etc, but here are some that I recommend:

-Big Whigs in the field

-Competitors (always good to know what they are putting out there)

-Your gene or protein

-Your field/subfield (I do a broad and narrow search)

-Collaborators (its sometimes nice to keep tabs on what these scalliwags are up to, when they aren't taking for damn ever to get back to you)

Hope this helps, I use this as a way to comb the literature without literally having to comb it, I just open up my inbox and the beautiful bounty of the aggregated pubs glows like the briefcase in Pulp Fiction.  I'm sure many PI's do this but I have known more than a few grad students and postdocs that had no idea of this and were manually searching every week or two for topics.

I'm lazy and if "If Mohammed will not go to the mountain, the mountain must come to Mohammed," then I let the PubMed citations come to me.

13 responses so far