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.

22 thoughts on “Back Door Method to Getting Articles in PubMed: Is Indexing so Important?”

  1. i published my paper in international journal but it stated that indexed in pubmed selected citations only… but my article not shown in pubmed search. can any one tell me how to add article to pubmed ? my research is carried out by self funding not by any funding agency support. is it possible to add into pubmed or PMC

  2. “submitted it to PubMed Central.” HOW does one submit to PubMed Central? Can you post the URL to the page where one does that?

  3. One thing that is useful for both websites is a tool called PaperFetch… it generates links to the PDF files directly from the PubMed search page.

  4. Re: research and patients – obviously this is important and I can see the benefits to the controlled vocab trees, esp for drug or gene names and other densely-linked terms. Since I don’t deal with patients and am not medically trained I have never encountered Medline at all. Perhaps those at NCBI or wherever need to make medline more explicit – similar to the “if you searched pubmed you would get XXX articles” that you get when you come to a result page from google.
    I agree entirely that naive google or pubmed searches are often less-than-adequate, as you have eloquently described. I think I shall find out where the library is and befriend my new institutional librarian.
    Access is a tricky thing – indeed, I think this is one area in which journal publishers will continue to have to work to maintain their prestige publications, through visibility via site subscription. Authors should also push for this, since it is easy to be mis-cited when someone is skimming an abstract, because they can’t get the full article easily.
    Overall, there is a balance between access and visiblity. If you have more access, then you might assume you can see more, but in reality, you probably stick to browsing the journals in your field and prestige/flagship titles. Everything else you get by searches. This is a similar situation as described by Eli Pariser, but even more dangerous, since in science we are all already field-limited so much.

  5. Your inadvertant analogy of Medline/PubMed to coke/pepsi and cola or soda may not find the health-favour with the medical community. However, a good point has been made in your write-up. Thanks.

  6. Hi Alan,
    MeSH are the official indexing terms by which all articles in Medline are indexed by. Why use specific indexing terms? Since you use Google you know that when you are searching for something like the drug Taxotere you will only get results where the specific term is used. You will not get results where they used the generic name docetaxel only. You will also not get any results that mentioned the broader taxene family of drugs. You will only retrieve web pages where the term Taxotere is mentioned and if they use it only a few times because they keep referring to it in the generic, then it my be a perfect site but it will be burried in Google rankings under junk that mentions Taxotere many times. So when you are searching Google you have to use both docetaxel and taxotere as your search terms and if you want information on the entire taxene family you need to include that term as well.
    However, you don’t have to do that when you search Medline if you use the MeSH indexing terms correctly. Breast Cancer is indexed as Breast Neoplasms. If you search using the MeSH index term of Breast Neoplasms you will retrieve all indexed articles regardless of how they referred to breast cancer in the title and abstract. By using the MeSH index term of Breast Neoplasms you will get articles where they used the terms breast cancer, breast tumors, ductal carcinoma, DCIS, invasive ductal carcinoma, etc. in the title or abstract.

    PubMed is the non-medical Medline, not the other way around. Everything in Medline is in PubMed but not everything in PubMed is in Medline. It is confusing. PubMed has the extra non-medical stuff like a Science article about the comet hitting the planet. PubMed may be the reconizable term but it is not Medline (although we use the two names interchangeably and erroneously) and it has stuff like non-medical stuff, ebooks, etc. that will never make into Medline.

    Ovid is a search interface to Medline. I prefer searching Ovid because it allows me stronger MeSH searching (I feel) and I can do adjacency searching (which can’t be done on PubMed). My boss likens searching Ovid Medline and PubMed Medline like driving a stick shift and an automatic. Both are cars and they will take you to your destination but depending on the situations one is better than the other for the drive.

    Most researchers like PubMed because most do their Google searches and are happy with the results. They may not find the best results but as you mentioned in your other comment, if it isn’t easy to get the article you aren’t going to read it. So if it isn’t easy to find the article they aren’t going to bother searching for it. Sorry but that isn’t exactly great research. Perhaps it is because I am a librarian and during my Masters degree program we focused on proper searching techniques and as a librarian I continually take CEs on refining my searching skills. Or perhaps I think it is poor research because I have seen one too many people get their articles rejected by journals because their research that they are doing is being done or has been done repeatedly elsewhere and somebody or somebodies have already written several articles on it. Perhaps if they did more than just a Google search on PubMed or consulted a librarian their research wouldn’t be wasted.
    On a more serious note, failure to do good research can lead to the death of patients. Everybody points to the Johns Hopkins incident where a healthy 24 year old woman died during a drug trial because the senior researcher didn’t bother looking at or getting older articles that mentioned the toxicity of hexamethonium and that hexamethonium was withdrawn from human use by the Food and Drug Administration (FDA) in the 1970s and had “never been approved by the FDA for administration via inhalation. But hey those were older articles that were hard to find and get.

  7. I would also say that I find that many of our medical students, residents, and faculty *really* love MeSH *once it is explained to them* in a way that is not library jargon-y. They really appreciate the feeling that they can make sure they’re using relevant terms, and it helps alleviate that “not sure I’m going about this the best way” feeling. Now, this applies only to the folks who are willing to acknowledge that they’re not already doing the best possible job of everything, of course. Obviously this also gets more mileage with people who are interested in being thorough or are really interested in a topic, not just “I need one thing to cite for whatever.”

    But I find that the “helps you figure out terms to use” approach (with a side of “building your search” and MyNCBI) is a good one and people can and do like it once they’ve heard it that way. Explaining it in the sense of controlled vocabulary, indexing, etc. though makes eyes glaze over.

    On the other hand, I will pretty much never utter the word MEDLINE to anybody, because I figure they just don’t need to know.

  8. Just another quick comment for publishers – if your article is behind a paywall, and my institution doesn’t subscribe, and I can’t find the PDF on google…. I don’t read your article. It might sound like the most appropriate article for my work ever, but there is so much info out there that I don’t have time to read, that I figure I miss a lot more than this one article every day. If it’s important, it will get cited or into a review somewhere soon, and I’ll get the gist then.

  9. I am a researcher (not a librarian) and I don’t understand MeSH at all. I use PubMed like google, and occasionally use google scholar, especially if I want a hard-to-get PDF. I don’t really know what OVID is, although I see it a lot when I am logging in to journal sites.
    For things in my field I get most through keyword-based RSS feeds from PubMed – are these based on MeSH? I don’t know, should I care?
    I have noted that Medline seems different to PubMed, but since they seem largely overlapping I have never been bothered to look deeper. I think this is likely to be a broader issue and to me as a non-medic Medline as a brand means nothing – PubMed is the recognisable term.
    I love PMC because you don’t have to go through all those annoying login screens etc – TBH, the biggest problem for me is not the searching (although, finding that one paper again, that you are sure you read last week is tricky), but the constant access screens and logins.
    Still, I remember the first (and only) time I used BIDS! It is certainly much better now.

  10. I note one thing to remember – you can only deposit your own paper into PMC if you have an NIH or Wellcome Trust grant ID. Papers supported by other funds are not accepted.

  11. Being able to explode and focus searches is an invaluable tool that requires indexing and which I could not live without.

  12. I only wish all researchers would give up the publishers and put their articles in PubMed Central. Maybe we will move to the prestige of publishing to be in PubMed Central and not a journal that makes all the money but gives none of it to the researcher.

  13. Just to poke the stick a little more at the post….

    As a librarian I care about the difference between PubMed and MEDLINE but I am also at fault for bluring the distinction in my general day to day conversation. When I am going to search MEDLINE, I most often say I am going to search PubMed. Like I said, the distinction between the two is eroding and it is becoming the Coke and Pepsi of the database colas.
    As a librarian I care about indexing. It brings organization to the potentially choatic arena of millions of records. It is an extremely powerful searching tool.

    But did you notice that I said, as a librarian? If you look at the email snippet I posted and listen/look at regular researchers…they don’t care about MeSH and the differences between PubMed and MEDLINE. They search using Google searches and to them the importance is to be in PubMed not necessarily MEDLINE. If they are in MEDLINE, great so be it, but they HAVE to be in PubMed.

    So again I am confronted with the question as to whether indexing in MeSH is going the way of the Dodo. Certainly only rare birds search by MeSH. I am also left asking about the MEDLINE vs PubMed ambiguity as well.

  14. I’ve explained the difference between PubMed and MEDLINE over and over again to numerous researchers, but the bottom line is that only librarians care! Well, librarians and anyone doing a systematic review.
    Indexing is an invaluable service that helps tame the chaos; the non-indexed stuff in PubMed is still a tiny minority that may or may not appear in anyone’s search.

  15. Great post! Thanks for sharing this example and clarifying the PubMed/PMC/MEDLINE landscape. I also love searching with MeSH. But it’s not like paint color: I love the green walls, but if you paint them blue that’s fine, too. The only thing that’s lost is my enjoyment. I love it because I can give a straightforward search strategy to my researcher interested in novel approaches to parasitic diseases who doesn’t know anything about your friend or the particular work that he’s doing on malaria.

  16. This exemplifies why we should search PubMed with words, phrases and MeSH to get all available citations. Understanding MeSH’s hierarchical arrangement is still crucial to successful searching and sometimes the addition of a subheading really represents your subject well, however, because of the inprocess and supplied by publisher entries, you must represent your ideas with words, phrases and MeSH.

  17. PubMed also has articles, journals submitted by the publisher – which may never be indexed, but do appear. To find them using Ovid, one of the Ovid Medline databases includes in process, publisher provided titles: Ovid MEDLINE(R) In-Process & Other Non-Indexed Citations and Ovid MEDLINE(R) 1948 to Present.

  18. There are a couple of other sets in Pubmed not indexed in MEDLINE, I think AIDSINFO and an old database of space medicine are a couple cool examples (maybe aids is indexed though, I’ll check on all this when I’m not on my iPod!). And this is actually a good way for medlibs w/ nlm or nn/lm funding to get their published lit in Pubmed (it’s what I did, or rather, had to do). But interesting question. What I think is interesting, too, is that publishers might now be more willing to put some effort into what NLM is constantly trying to communicate: highlight the fact that Pubmed is not MEDLINE (in order to keep their prestige), accept no substitutes. :). (Sidenote: your researcher’s article would likely not be found by my clinical users, who often go through OvidMEDLINE, for whatever reason.)

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