Back Door Method to Getting Articles in PubMed: Is Indexing so Important?

A very good friend of mine is a professor who researches and writes a lot on malaria.  He emailed me this morning to tell me that he had recently published an article in a journal that was not indexed in MEDLINE, but he was able to get the citation and abstract in the PubMed database anyway. 

His research is funded by the NIH and the article he published is open access, so he made it available for immediate release and submitted it to PubMed Central.  Voila, his article, although not indexed, is in PubMed. 

He ended the email saying, “You probably knew this but how come we are never privy to this trick.”  This is where I am embarrassed to say that I did not know you could get an article published in a journal not indexed in MEDLINE into PubMed by sumitting it to PMC.  I had no idea.  I knew there were non-indexed articles in PubMed, but I always understood those to fall into two categories, 1. new and waiting to be indexed 2. articles in indexed journals that aren’t medically related…for example Dynamics of magnetic domain walls under their own interia. Science. 2010 Dec 24;330(6012):1810-3 is in PubMed but isn’t indexed.

I had no idea that PMC articles were automatically added to PubMed.  I always thought PMC articles were in journals indexed in MEDLINE that were OA.  Now, my friend said in his email that he got his article indexed in PubMed.  He was wrong, the article is not indexed.  If you search for it in PubMed using only MeSH terms or if you are like me, an avid Ovid user, and you don’t often search the Ovid MEDLINE In-Process & Other Non-Indexed Citations file you are going to totally miss that article.

Early librarian me probably would have been extremely concerned because the article wasn’t indexed.  However, how important is indexing when you can get your article in PubMed anyway without indexing?  Let’s face it normal people don’t search PubMed correctly.  Almost every library user I see searching PubMed is doing their Google style searching in the database.  A simple Google search for malaria and my friend’s last name retrieved the article immediately (top result since it is a 2011 article). 

The article isn’t indexed in MEDLINE yet it is totally retrievable through PubMed and that is the DOC (database of choice) for biomedical researchers.  Researchers’ understanding of the differences of being in PubMed vs. in the MEDLINE database are already extremely blurry.  They interchange the two terms (and librarians do too) when in fact there is a technical difference.  PubMed and MEDLINE have become the Coke/Pepsi of medical databases.  Two different products but people use the terms interchangeably when ordering a cola soft drink. (Don’t even get me started on the Pop vs Soda debate.)  As I mentioned, you have an ever growing group of users who do keyword searching on a structured vocabulary database. 

So what is the value of being in MEDLINE when you are in PubMed and what is the value of having a journal article indexed when people don’t search that way anymore?  All scientists want is for their research to available to be read and cited.  Getting an article in PMC does that.  Perhaps it is time for us to let the indexing go.  Wow I can’t believe I am saying that as a librarian because I love using MeSH to search.  But, just because we love something doesn’t mean that its time hasn’t past.


My friend gave me permission to repost his email to the blog, to better understand how he as a researcher feels about the whole thing.  (All identifying information has been removed or changed.)

From my end, the NIH really cares that you have a PCMID (and a link to the pubmed page) for all manuscripts on your Biosketch or the paper doesn’t count. At least they are heavily moving in this direction to keep people more honest.

 Also who cares if the MESH terms didn’t get indexed; the title, author names, and the entire abstract did.  My MESH terms would have been earth shattering terms like, malaria, antimalarial drug discovery, new drugs etc. all of which are in the abstract.

 I found it all these ways by searching for: My name, Part of the title, Sentence from the abstract, and keywords

It is searchable from Google Scholar and is in Ohiolinks now too.

 All of which is nice because now people can find it and cite it (infact someone already has). And now that it is in PMC they can read it easily, more so than other articles which are not in PMC or open access.

Basically all he wants is the PCMID and his journal to be findable in PubMed (which it is). As he mentioned he doesn’t care about MeSH.  Hmmm something to think about librarians.

Confusion on Withdrawn Article from Cochrane

Yesterday I had a request to do some sleuthing on the article,”Androgens versus placebo or no treatment for idiopathic oligo/asthenospermia. Vandekerckhove P, Lilford R, Vail A, Hughes E. Cochrane Database Syst Rev. 2007 Jul 18;(4):CD000150.  In the PubMed citation there is a nice big WITHDRAWN in front of the title.  The doctor wanted to know why the article was withdrawn.

My first stop was The Cochrane Library on Wiley.  According to The Cochrane Library,”This review has been withdrawn from The Cochrane Library as it has not been updated since 1996.”  Ok makes sense, if the review article hasn’t been updated in that long then I can see withdrawing it.  However, I began to look a little more and of course got a little more confused.  Apparently another review article (same title, authors, and CD#) was published in 2000 and does not have giant WITHDRAWN printed in front of the title on the PubMed citation.

So my brain started to ask the questions…

  • If the 2007 wasn’t updated since 1996, was the 2000 article updated?
  • Why is it when I search for the 2000 article in PubMed there is no mention of it being withdrawn, but when I search The Cochrane Library for both the 2000 and 2007 review articles (both have the same CD#), the databse tells me it is withdrawn? 
  • Shouldn’t PubMed have a big ol’ withdrawn next to the 2000 citation too?

Another question that is bouncing around in my head is in the wake of so many scandals regarding scholarly publishing, were the 2000 and 2007 articles ever updated from 1996?  The way The Cochrane Library has it listed it makes me think not.  Because The Cochrane Library says the article hasn’t been updated since 1996 makes me believe that the original review article was written and published in 1996 or before.  However when I search PubMed there are no articles by these authors on this topic before 2000.  Yet when you look at the 2000 citation it clearly points to a 1996 article:

Cochrane Database Syst Rev. 2000;(2):CD000150. Review. Update in: Cochrane Database Syst Rev. 1996;(4):CD000150.

Obviously the 2007 review article has been withdrawn and I would be hesitant to use the 2000 one as well.  But it is a little hard to figure out the story behind the withdrawal, other than it hadn’t been updated since 1996.  But there are still a lot of questions left hanging out there.  Now that things are going more digital it seems the breadcrumb path of the article is more nebulous which makes it difficult when those articles are no longer appropriate to use for treatment decisions.

Good Example of Phrase Searching in PubMed

Just like some people like their cars to have a manual transmission while others prefer automatics, librarians tend to fall into one of two MEDLINE camps, those who prefer Ovid and those who prefer PubMed. 

I am an Ovid kind of gal.  Don’t get me wrong I can do a PubMed search and have done them and still do them frequently when I need to, but my MOC (MEDLINE Of Choice) is Ovid.  Since I am in Ovid often enough I tend to see and remember better certain things in my daily searches that might be good teaching methods or examples . 

Because I am not in PubMed as often as Ovid, I don’t have the experience of running across good search examples that I can pass on or use while teaching.  That is why I try and pay particular attention to good PubMed teaching examples as the come up.  I either try and blog about them, tag them, or print them off and save them for later. 

The NLM Technical Bulletin has a nice example of how to do effective phrase searching in PubMed.  This is nice because certain things like “text messaging” (their example) are best searched as phrases.  As the Tech Bull notes it is important to look at the Search Details to know whether your term is being applied in the MEDLINE database as you want/think it to be. 

Really I tell everyone when I teach PubMed to look at the Search Details.  Sometimes I wonder how much they really do that or whether the nodding of their head is not in agreement with my point but instead to the beat of some song they have stuck in their head.

Non-English Guides for PubMed

Those of you in other parts of the world or who work with a lot of international medical professionals who might prefer to learn PubMed in their native language you might be interested to know that the National Library of Medicine has several PubMed guides in other languages other than English.

Information is available in:

  • Chinese / 中文
  • French / Français
  • German / Deutsch
  • Italian / Italiano
  • Japanese / 日本語
  • Norwegian / Norsk
  • Portuguese / Português
  • Russian / Русский
  • Spanish / Español
  • Vietnamese / Tiếng Việt
  • Go to

    Friday Fun: NLM Milestones

    According to the Technical Bulletin, PubMed has added its 20 millionth citation and PubMed Central has logged its 2 millionth article.

    I almost feel like their should be some balloons falling from the ceiling, noise makers whistling, and confetti and streamers flying about to celebrate the occasion.  Perhaps this is because I am a nerdy librarian who thinks 20 million citations is cool.  Or it could be because I missed the party entirely (the bulletin mentions this actually happened in July.) Oh well.

    Happy Belated 20 Millionth! 

    If you want to read a brief history about PubMed, go to the Technical Bulletin.