PubMed Centeral Name Change

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.

PubMed Limits to Replace with Filters Sidebar and Author Ranking

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.

What is a disaster and what are your plans?

I think we all can agree that something like fire, tornado, flood, earthquake are all disasters and hopefully libraries have some sort of contingency plans when those events happen.  But what about those “other” disasters.  I say other because they may not meet the standard definition of a disaster, but when they happen all work stops or something majorly impacts your productivity.

Marie Kennedy posted “Disaster planning for e-resources” on Organization Monkey about her library’s recent problems when EBSCO’s databases went down earlier this month.  “From a library perspective, when a major content provider goes down, it is a legitimate disaster. For electronic resources librarians, all the usual work stops and crisis management mode takes over.”  This is true for us as well.  Even if a major journal goes down we start getting calls right away from doctor’s wondering what happened.  If our linking system goes down or a major database goes down, then all *blank* hits the fan. 

Our operations are so dependent on certain programs that when they go down our access to information also goes down.  It may not be a disaster in the traditional sense of the word, but it is still a disaster for information retrieval. 

Marie describes the procedures her library use to inform library personnel and library users of situation.  She also mentions how frustrating it was for her and her library’s staff to go through this “without the help of EBSCO.”  In fact most librarians were reaching out through MEDLIB-L, Twitter, and other local listservs,  to try and figure out why CINAHL, Discovery, and other resources were DOA.

EBSCO is just the latest resource, but this sort of things has happened with Ovid, PubMed and other databases or online journals.  It also won’t be the last resource to experience a “temporary outage.”  So what are your library procedures for dealing with these events?  How do you notify your customers and does that vary according to the resource?

Versioning in PubMed

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).

  1. Search via the PMID number for the specific version. Example 20029611.1
    The .1 represents version 1.
  2. Search via the PMID number for any version. Example 20029611.*
    The * is the wildcard.
  3. 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.

Get Paid to Help Create a Next Generation Resource Tool

InContext is partnering with LWW/Ovid to redesign the next generation of electronic information resources for medical professionals.  Based on previous in-depth observational interviews, InContext has proposed some solutions and ideas to better support people who access journal articles online or conduct literature searches.  Because this is a “next generation” project, InContext is especially interested in working with people who own and smartphones and/or tablets  for work or personal use. 

They are testing their ideas for this next genration project by conducting in-person, paper prototype interviews.  The interviews normally would take 90-120 minutes.  Ovid/LWW is offering an honorarium for participation.  They will be doing interviews March 15-20 and March 29-April 4.

If the idea of being on the ground floor to help shape and create a better tool for accessing online journal articles and conducting literature searches is interesting to you AND you like getting paid for your ideas, then go to to see if you qualify to participate.

e-Books: Why Bother

I had a great idea.  Or at least I thought it was a great idea.  However making it a reality makes me think that maybe my idea might just stay in the realm of ideas.

I have mentioned in previous posts that I swear a boat load of people got iPads or smartphones for Christmas because the calls for help about resources, ebooks, network access, etc. have really taken off. Some things like network access or knowing how much data they might consume if they are doing 3G are a little bit out of our control.  But ebooks and library resources, well hell, I thought I could help with that in a relatively easy way.  (Just hit me over the head if I ever think something is going to be easy.)

We are in process of re-designing our website so we did a survey of our users.  We learned that 53% surveyed agreed or strongly agreed that a website for mobile use of library resources is important.  We learned that our users want a website with; better organization, streamlined function, easy for tech un-savvy, and fewer clicks to get to resources.  They want a simple way to find books and ebooks.  (Clearly the catalog isn’t what they consider simple.) They want an easier way to login to resources from home, and to login once.   Not only do our users want simple easy ways to access online resources from the website and their mobile devices but they want simple (few clicks, easy one login) to ebooks from home. 

Ok, now we’re cooking. We know what our users want, so let’s get going. Somebody is working on the regular website and I thought I could help get things mobile.  I approached it on two fronts, the mobile resources and easier access to ebooks.

Lots of librarians shared their lists on Medical Librarian Forum and we have been compiling a list of mobile friendly resources.  Not only would we have a list of mobile friendly sites and apps the library subscribed to but we would have our own mobile site linking to the mobile friendly library resources.  Additionally we came up with a few ideas on how to increase the visibility (and hopefully the usage) of our ebooks. 

I was feeling pretty confident that these things could make finding ebooks easier and also help current and future mobile users get to our resources.  Remember, I said I thought it would be easy? Just start hitting me on the head now…

The problem is the mobile site of vendors.  Many vendors like Elsevier (MDConsult and First Consult), McGraw Hill (Access database) direct smartphones immediately to their mobile site.  While this is nice, their mobile sites require users to login  using their personal login they created.  So a library user would have to have a personal login to each database: MDConsult, First Consult, and all of the Access databases we subscribe to.  If somebody is accessing our resources off campus these personal logins are needed in addition to our proxy login that our users already use to access library resources from home. 

See the problem?  People who are just browsing our resources on their smartphone on campus have to create multiple logins in order to use our online resources from their phone.  We link to our ebooks through the catalog and we are thinking about adding QR code browsing of ebooks in the stacks, but this won’t work on smartphones.  Why? Because when the person scans on the code or clicks the link in our catalog the vendor’s mobile site demands a personal login.  So there is no direct link to the ebook, they have to have a personal login.  Most users don’t think of our ebooks according to vendors, they just click on the title and they EXPECT the book to show up, they don’t expect to be asked for another login.  This method assumes our users have created a personal login with that vendor prior to clicking on the book.  Most people aren’t thinking, “Oh I want to look in Harrison’s Online, I should get a MyAccess login before I click on the title.”

The problem gets even more compounded when our users are off campus.  Our users have been trained to login to our resources using our proxy server.  This is what they have been doing for years, it is a standard for accessing resources remotely, and this is what most users want.  In fact respondents to our recent user survey said they want one login! Well, we can’t provide that if the vendors are creating an extra login! 

So even if I want to provide easy access to ebooks, I can’t.  I have remind people that they have to create a personal login with each vendor.  How do I do that?  That is a heck of mess to write in the online catalog record for each title.  “Click here for access. If you are using a smartphone you must login with your personal login.”  Great then I get more calls about how to create a personal login, to reset their personal login, or that they are using their personal login and can’t get in (but they are using their proxy login). 

Not only do I have the problem in the catalog, I would have the same communication problem on the mobile library site. As anybody who has a smartphone knows, mobile optimized sites are easier to view than the full website.  So the design is a little different than a regular website.  For example if you are linking to resources, you probably don’t want  a whole lot words explaining things.  People on a mobile library website really kind of want the links to go to the resources they need not a whole bunch of instructions about unique login procedures for each resource.

As somebody mentioned to me users don’t have to have a personal login they just tap on the link to Full Site and they can access the resources.  Um doesn’t that kill the whole point of having mobile optimized resources?  Searching th full site of MDConsult or AccessMedicine on a smartphone involves a lot of screen expanding and pinching.  Aren’t we trying to get our users to use our ebooks?  Aren’t we asking/demanding vendors that our ebooks also become mobile optimized?! 

Locking ebooks behind personal logins or forcing people to use the Full Site is not getting people to use the ebooks or online resources. It is a barrier!  Why have vendors created this artificial barrier?!  Why can’t an institutional user access an online resource or ebook without having a personal login?!

In addition to the user access problems I have with personal logins, I have two other questions/problems…

  • Usage stats – Are we getting usage stats each time somebody from our institution is using their personal login? If no, that is very bad. If yes, that is good but we can get without personal logins. You already have our IP ranges and proxy info.
  • Concurrent users – If you don’t have an site license then people can easily come as visitors create a personal login and then use that personal login to access your material looooong after they have left your institution.  These unauthorized unaffiliated users are taking up your concurrent user license spot(s).  We maintain our authorized users list.  We enter the expiration date of visitors, students, contractors, techs, etc. into our system.  When their badge expires they can’t access our resources via proxy.  Therefore we are in agreement with our license agreements AND they are taking up a concurrent user spot.

It is possible to have the mobile site work using institutional proxy, Thompson Reuters Web of Science is mobile optimized.  I click on the link to WoS and I am directed to the mobile site. I am not asked for a personal login.  Off campus I am asked to login to my library account then I am directed to mobile site.  Easy squeazey and MAKES SENSE!

What started out as an easy (yes keep hitting me on the head) project of providing a simple list of mobile optimized resources and linking directly to the books turned into a giant mess.  How can I recommend these mobile resources to smartphone users or the ebooks when I know it will confuse them and frustrate them.  Hell, it confused and frustrated me and I am a librarian who is FAMILIAR with this stuff.  Our users aren’t going to use this stuff the way it is set up right now and unfortunately I can’t make it easier for them because this personal login thing is out of my control.  Why should I bother setting up links to mobile resources and ebooks when it is going to cause more problems and questions then it is worth and serve as another reason to bypass the library for stuff.  No wonder people get their ebooks from Amazon….it is EASY!  Easy is what the users want, medical library ebooks in their current state are not easy, they are a royal pain. 

Why bother?!  We try to make things easily available and barriers keep getting thrown up.  It is enough to drive you batty.  According to ReadWriteWeb, mobile Internet usage has doubled every year since 2009….so this problem isn’t going away.   Hopefully in the near future I won’t be asking why bother with the mess of ebooks.

New PubMed Tutorial

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.

MEDLINE End of Year Processing Information

NLM is involved in MEDLINE year-end processing activities which include changing MeSH, Substance Names and other global changes.  This always causes a temporary suspension in indexing citations. 

So here are some important dates to note:

  • November 16, 2011: NLM expects to temporarily suspend the addition of fully-indexed MEDLINE citations to PubMed. Publisher-supplied and in process citations will continue to be added.
  • Mid-December 2011: PubMed MEDLINE citations, translation tables, and the MeSH database will have been updated to reflect 2012 MeSH.

For details about the impact on searching from November 16 to mid-December, see: Annual MEDLINE/PubMed Year-End Processing (YEP): Impact on Searching During Fall 2011.

For background information on the general kinds of changes made annually, see: Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information.

My NCBI Enhancements

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.

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.