Ok I tried to read the NLM Tech Bull, New PubModel for PubMed Citations, but it was so packed full of jargon that my brain started to hurt. I read it through several times then asked our cataloger what she understood of it.
This is what I was able to piece together. It is for online only journals and they will have two dates, the eCollection and the published date. The eCollection date refers to when the article was deposited in PMC.
I have several thoughts…none of them pleasant.
First, it is pretty bad when the technical bulletin is confusing to the very readers it aims to inform. I am not the only one who thinks it was confusing. Check out these responses to my quick question on Twitter.
Second, isn’t the term Electronic eCollection kind of redundant?
Finally, Does this solve the epub ahead of print mess or just add to the confusion? To me it seems to add to the confusion. Not only do we have 2 different possible “publication” dates but their example article “was published online on January 25, 2013, yet was included in the Volume 3, 2012 collection as deposited in PMC.” Does anybody find that absolutely confusing?! What is the correct citation for authors to use?! When was it really published? Why is PMC not listing it when it was actually published by the journal on January 25, 2013!?
How can I explain this to doctors when I can’t understand it and why it is being done? Please somebody comment because I befuddled.
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If you haven’t heard about the Mayan civilzation’s calendar predicting the end of the world on December 21, 2012, then you have been living under a rock. Personally I believe the Mayans were on to something. Instead, I believe the end of the world will happen on January 1, 2013. Why?
As of January 1st NCBI will no longer support Internet Explorer 7 and all the hospitals that haven’t upgraded will begin to have problems searching PubMed. You can’t blame the Mayan’s for not warning us. I think they were pretty close to their prediction considering that browsers and the Internet were not known in AD 250. I just think all of the doomsday prophets just translated things wrong (wouldn’t be the first time that happened).
The end may not come as a big bang right on the New Year, but as NLM makes enhancements and changes to NCBI the people in the IE 7 hospitals will begin to have problems with PubMed. http://www.ncbi.nlm.nih.gov/guide/browsers
The compatibility issue is just going to continue on. The newly launched PubReader hasn’t even been tested on Internet Explorer and from the looks of the browser compatibilty chart they aren’t dilly dallying around with IE 8 or 9, if they design for Explorer they are going straight for IE 10.
Since PubReader was “designed particularly for enhancing the readability of PMC journal articles on tablet and other small screen devices,” the compatability for desktop and laptop browsers may not be an issue for a while.
But this brings up the issue of IT departments needing to update the browsers. Many librarians I have communicated with have expressed how getting IT to upgrade anything (including browsers) is a monumental task. Just from my average web browsing it seems to me that a lot of web sites are jumping from IE 7,8 to IE 10. Even more frustrating/interesting for hospital librarians is that there seems to a growing number of people not even designing for Explorer.
Knowing who is winning the browser wars is tricky and getting good data on browser market share really depends on the site that measures market share. Network World’s article “Browser battle: Chrome vs. Firefox vs. IE vs. Opera,” says “it’s difficult to say who’s on top in this four-way scrap. For one thing, different methods of measuring market share often provide very different numbers – while data from NetMarketshare.com shows IE in front with 54% of the market for October 2012, StatCounter gives a slight edge to Chrome, about 35% to 32%. W3Schools’ information paints another picture again, showing a big lead for Chrome (44%) over about 32% for Firefox and just 16% for IE.”
It may just be me and my apocalyptic Mayan frome of mind but I am thinking of the Thunderdome for browsers. Although saying “Four browser enter, one browser leaves” isn’t as cool as Tina Turner’s line, “Two men enter, one man leaves.”
Basically with the amount of browsers vying for for top spot it makes it difficult for us and IT to keep up. So it is easy to see how people can be in this predicament. So instead of stocking up on food and water in anticipation of the end of the world, start working on your IT department to upgrade your browsers.Share on Facebook
Over at the Scholarly Kitchen, Kent Anderson writes of his frustrations regarding PMC, PubMed and MEDLINE and non indexed journals (particularly the start up journal eLife) in his post, “Something’s Rotten in Bethesda — The Troubling Tale of PubMed Central, PubMed, and eLife.”
I find myself both agreeing and disagreeing with Anderson.
I agree there is a big problem with the blurring of the lines in the minds of most people (mainly doctors and researchers) regarding PMC, PubMed and MEDLINE. PubMed houses the citations for PMC articles as well as the citations to articles in journals indexed within MEDLINE. The problem is that to most normal people PubMed = MEDLINE. I mention the blurring of the lines between PubMed and MEDLINE in post “Back Door Method to Getting Articles in PubMed: Is Indexing so Important?” In my post I mention that doctors and researchers think of PubMed and MEDLINE as the same. I likened it to ordering a cola. “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.” I even posted the email of a researcher friend further illustrating how they don’t distinguish between PubMed and MEDLINE and if the article is PMC it is in PubMed and that in their minds it is in MEDLINE. At the time of my orginal post I questioned the point of actually indexing journal articles since researchers don’t search by index terms and they erroneously think PubMed is Medline. All they have to do is get into PMC and it can be found in PubMed via keywords (which is how everybody searches these days).
Anderson’s main argument is NLM is acting as competitor to publishers and technology companies, by allowing certain journal publishers to bypass rules for inclusion into PMC and PubMed. In his argument he brings up the journal eLife a “fledgling funder-backed journal” that was allowed include articles in PMC despite not having published the required 15 articles, not being indexed in MEDLINE, and PMC acting as the sole provider of the articles. Not only is NLM circumventing the rules for inclusion to its databases but he believes that NLM is acting as the primary publisher to eLife because their articles can only be found on PMC. Anderson uses JMLA and Journal of Biomolecular Techniques as other examples of journals that NLM acts as the primary publisher. I don’t know anything about the Journal of Biomolecular Techniques but I disagree with JMLA serving as an example similar to eLife. As I mention in my comment to his post on Scholarly Kitchen, JMLA has been around since 1911 so it has fulfilled the 15 article requirement and is published by a publisher (who is not PMC) and sends me the print 4 times a year. The journal is indexed in MEDLINE (since 2002). Additionally the printed edition clearly states that the digital archives of JMLA are on PMC. I went to PMC today (October 22, 2012) and the October 2012 issue is not available. So the most recent issue is not online and PMC is acting as the a digital archive. Therefore NLM is not acting as the publisher of JMLA in the way he describes. In the case of JMLA NLM’s PMC is the secondary publisher that he describes, which is the case of many indexed MEDLINE journals.
Unfortunatley I think Anderson’s argument misses a bigger issue. The question of quality within the PubMed database. As I mentioned there is confusion among PMC, PubMed, and MEDLINE. People searching PubMed will find an article from the PMC that is in a journal that is not indexed in MEDLINE. However people will erroneously think the article and and journal are in MEDLINE when in fact they are just in PMC. By allowing non indexed journals into PMC, NLM is basically allowing a back door into PubMed, and by default into MEDLINE. Of course NLM doesn’t see it as that, because they are one of the few people who can still see a distinction between PubMed and MEDLINE. Their users (doctors and researchers) do not see the distinction. To them PubMed is MEDLINE. This calls into question the quality of the articles in PMC in journals that are not indexed in MEDLINE. If the journal isn’t good enought to get into Medline then why is the article good enough to be found in PubMed?
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According to the NCBI Website, the NCBI resources will no longer support IE7 after January 1, 2013. So medical librarians in Internet Explorer institutions, now is the time to start talking to your IT departments to get IE 8 or greater, or Firefox 4 or greater installed on your computers.
This means that after January 1, 2013 if you are searching PubMed using IE7 and something goes wonky, it is your problem. They will no longer design PubMed so that it will work using IE7.
For information on other browsers like Chrome, Safari, and Opera check out the NCBI browser check list.
On a medical librarian related note, MLA’s site gets fussy using IE 7 and 8. Bascially Internet Explorer is a frustrating browser to design for because there is designing for the rest of the web then there is designing for IE. I am told IE 9 is better, but it is probably worth trying to get Firefox or Chrome added to your computer if you can. However, it all depends on your IT department and their policies. So pick your battle to at least make sure whatever browser you are allowed to use is compatible for the NCBI resources.
**Update 8/21/12 10:48am)**
ACGME won’t work with IE7 after September 1, 2012. For more information on other browsers and versions go to:
http://www.acgme.org/residentdatacollection/documentation/browser_requirements.aspShare on Facebook
PubMed Central apparently was often confused with PubMed, so NLM has decided to change its name to just PMC. According to the Tech Bulletin PMC has a new look and feel to go with its new name. The redesign is an attempt to present a “cleaner and more uniform presentation across PMC’s site as well as its article, issue, and journal archive pages.” Pictures of the redesign can be seen on the Tech Bulletin page.
Other improvements include:
- New links for article front matter such as article notes, copyright and license information
- Views for tables and figures have been improved
- Easier readability, navigation, and linking within the new article page
- Enhance bibliographic citation look
- “Go to” navigation drop down menu linking to sections within the article
Other improvements will be coming and will be featured in future Tech Bulls.
I have only one small gripe. It is with the changing of the name from PubMed Central to PMC. If NLM intended to try to eliminate confusion with PubMed, I don’t think changing the name to PMC will do it. Unfortunately, I feel PMC is still too close to PubMed and the name still doesn’t really tell people what the product is to differentiate it. It really needs a name that indicates it is an area that contains fulltext articles in PubMed. (Even that is slightly a misnomer because there are full text articles to journals not in PubMed…but only geeky librarians and NLM really know that.) Something like PubMed Full Text Archive, while not exactly short and sweet is more descriptive and less open to confusion than PMC.Share on Facebook
PuMed will get a new look soon. The May/June NLM Technical Bulletin announced the Limits page will be replaced by a results filter sidebar. The filter sidebar will work the same way as the limit selections page. For pictures on the upcoming change go to the Tech Bull.
Additionally the PubMed default Review and Free full text filters will also be moved to the filters sidebar. Filter your results portlet will eventually be added to the filters sidebar too.
The PubMed Abstract display will soon also be displaying author results using a ranking algorithm when searchers click on the author search link. This change was done to try and help deal with articles from authors of common names.
See the Tech Bull for pictures and a better explannation.
When you click on an author’s name in the abstract display, PubMed conducts an author search. In the past if you clicked on Smith, J. You would get a list of all article by every Smith, J in publication date order. With these new changes, “If an author name is computationally similar to an author name for additional PubMed citations, the results will display those citations first, in ranked order, followed by the non-similar citations. The results sort notation will display as ‘Sorted by Computed Author”
If I understand this correctly PubMed will look at the original Smith, J article and compare it with other Smith, J articles and displays the citations to article that the orginial Smith, J probably authored ahead of others he might not have authored. So if you are looking for articles by the cardiologist Smith, J the article citations for the urologist who is also Smith, J won’t appear at the top of the results.
Since most people tend to publish in their own area of expertise this should be helpful. The only thing you have to do is make sure you account for those times where they publish outside of their usual field.
Of course all of this would be moot if NLM would adopt standard author ID numbers like other databases have done.Share on Facebook
I am really late with this news, my apologies. A colleague of mine brought this to my attention. According to the February 2012 Technology Bulletin, PubMed no supports versioned citations. “Revisions, scientific updates, and updates of reviews are examples of content that could be versioned. Versions are not intended for correcting specific errors in an article, for which published errata notices should continue to be used (see Fact Sheet). ”
As each article is updated the next version will be placed in PubMed with a label next to the journal title indicating the version. (Version 2, Version 3, etc.)
I guess the good news is that only the most recent version will be indexed and found in PubMed using normal methods (even Googly type searches that really normal people do). So you won’t be seeing multiple versions in a results list. Thank God.
You can search for older versions by using three different searching techniques (See Tech Bull for images).
- Search via the PMID number for the specific version. Example 20029611.1
The .1 represents version 1.
- Search via the PMID number for any version. Example 20029611.*
The * is the wildcard.
- Search via topic and the click on Other Versions link at the bottom of the abstract.
It is important to know that authors do not cross versions. What I mean by that is if Michelle Kraft was an author in version 1 but not an author in version 2, you can’t do an author search and retrieve the version 1 citation. My version is lost if you search via my name. I predict this to be a bit of a problem. There are too many doctors and institutions that keep track of their publications and when you start telling them their article (no matter if it has been superseded) is not able to be seen by searching their name, it isn’t going to go well.
So if you don’t have the PMID number it is going to get clunky to find an older version. If you can’t find a citation you have to double check the citation (spelling, numbers, etc.) but now the possibility lies that you retrieved no results because it is an older version, NOT because the citation is incorrect.
There are also some funny things going on with date as well that people should be aware of. “PubMed will set the DateCreated for the new version to the date the citation is added to PubMed. We will retain the Entrez Date, which defines the display order in PubMed, as the original date unless the publisher supplies a new PublicationDate. If the PublicationDate on the new version is different, we will modify the Entrez Date so the citation will display at the top of the search results.”
I understand and like the idea of having different versions within PubMed, but I am not sure this done in the best way. I think you need to be able to find older versions other than just by knowing the stupid PMID number. How many people know the stupid PMID number. Usually we librarians are verifying the citation to GET the PMID number. I think you should be able to do an author search and retrieve the older version. Now there should be some serious marking on the citation indicating it is an older version and a new version exists (way more markings than NLM will slap on a citation). By not including the older version of an article when doing an author search, not only are they saying to the authors that their article has pretty much disappeared but it makes finding articles from a citation list a real pain in the butt as well. There are lots of researchers who look at the citations at the end of the article for their own research.
What do you think? I am not as big of a PubMed searcher as other librarians. I am an Ovid gal (thinking how this will effect searching Ovid MEDLINE hurts my brian too much) so there are others with much better PubMed searching skills and I would love to hear there thoughts.Share on Facebook
A new PubMed Tutorial is available. This tutorial was updated in December 2011, and reflects PubMed changes through December 12, 2011. To see a list of recent PubMed changes, go to PubMed’s New/Noteworthy.
Those of you who create your own PubMed tutorials unique to your institution’s settings may want to view this new one to see if you need to change or update anything.Share on Facebook
The June 24, 2011 NLM Technical Bulletin reported on some enhancement to My NCBI’s My Bibliography. My Bibliography will soon display links to free full text, related citations, and articles cited in PMC. It will also have a “portlet” for related PubMed citations. The citations in the portlet will be based on topics of the citations that are stored in My Bibliography.
For more information including a picture of how it will look go to the NLM Technical Bulletin.Share on Facebook
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 pubmed.gov 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.Share on Facebook