Databases

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that keep track of their publications and when you start telling them their article (no matter if it has been superseded) is not able to be seen by searching their name, it isn’t going to go well.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.

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1 comment - What do you think?  Posted by KraftyLibrarian - March 27, 2012 at 11:20 am

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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 http://www.surveymonkey.com/s/LWW_Study to see if you qualify to participate.

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1 comment - What do you think?  Posted by KraftyLibrarian - March 8, 2012 at 1:49 pm

Categories: Databases, Ovid   Tags:

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 iMedicalApps.com 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.

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6 comments - What do you think?  Posted by KraftyLibrarian - February 7, 2012 at 12:07 pm

Categories: Databases, Electronic Access, Journals and Books, SmartPhones, Technology   Tags:

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.

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Be the first to comment - What do you think?  Posted by KraftyLibrarian - December 19, 2011 at 2:40 pm

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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.

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Be the first to comment - What do you think?  Posted by KraftyLibrarian - September 6, 2011 at 2:21 pm

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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.

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Be the first to comment - What do you think?  Posted by KraftyLibrarian - July 6, 2011 at 10:29 am

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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.

—-Update—–

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.

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17 comments - What do you think?  Posted by KraftyLibrarian - June 15, 2011 at 12:03 pm

Categories: Medline, Ovid, PubMed   Tags:

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.

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2 comments - What do you think?  Posted by KraftyLibrarian - June 7, 2011 at 2:47 pm

Categories: Medline, PubMed   Tags:

Web Tools For Searching Biomedical Literature

Have you heard of iPubMed, PubGet, Bablemesh, HubMed?  They are some of the many alternative interfaces to PubMed, offering different search and retrieval methods currently not available within PubMed.  With some many of these aternative interfaces how do you keep track of them?  When would it be better to use the alternative interface over PubMed or vice versa?

John Dupuis alerted me to this article, “PubMed and beyond: a survey of web tools for searching biomedical literature” (free full text) from Database (2011) Vol. 2011, doi: 10.093/database/baq036

The article looks at and reviews 28 web tools for searching the biomedical literature and compares them to PubMed and each other and has a website dedicated to tracking existing tools and future advances in the area of biomedical literature search tools.

Abstract:

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field.

Not only does the article look at these 28 interfaces but it also looks at the recent changes to PubMed that were often influenced by these and other outside interfaces.

There is no way any library or librarian can teach or support every one of these interfaces, but this paper is free and is a nice resource to whip out when somebody asks about one of them.

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4 comments - What do you think?  Posted by KraftyLibrarian - April 28, 2011 at 4:41 pm

Categories: Medline, Technology   Tags:

The Mobile Web Is Not An Alternative

Wednesday’s post on medinfo alerted me to this interesting article in The Chronicle of Higher Education, ”As the Web Goes Mobile, Colleges Fail to Keep Up.”  The article states that more and more college students access the web using the mobile devices.  From the graph in the article, in 2010 43% of college students use mobile devices daily to access the Internet compared to 10.2% in 2008.  That is a huge jump in mobile web usage.  Yet according to the article many colleges “treat their mobile web sites as low-stakes experiments.” 

Of course right away my mind is thinking, “If colleges are treating the mobile web as a low stake experiment, what are the libraries doing?”  Depending on the library’s relationship with the college, it may beholden to the college IT department or it may have its own IT department.  That relationship will help drive a lot of the mobile web direction.  However, what is also driving the libraries’ mobile web direction are the library resource vendors.  How many ILS systems have GOOD mobile web platforms?  In the days of shrinking budgets (state and institutional) how affordable is it to add these ILS companies’ mobile platform to the library’s system?  How can a library justify that extra cost when it is faced with a flat or shrinking budget and may have to cut journals, books, hours, staff, etc? 

How many databases and online books are available/optimized for mobile devices?  Let’s ignore the Nook and Kindle like devices, students ARE NOT using them as mobile devices.  They aren’t carrying them around all the time like they are their smart phones.  They are going to use their smart phones to order Chipotle, text a friend about meeting up or an upcoming test, then they are using it to do research (usually on Google) to find a title/resource and read it.  So how many online medical text books are smart phone optimized?  Not many.

Libraries are beholden to not only their institution’s response to the mobile web but also to their own profession’s resource vendors’ response.  I remember talking to one rather high ranking sales rep for a major medical database/journal/online book provider.  I asked him if his company had created an mobile optimized version of their search database and whether there were plans to gradually optimize their many online books and journals.  He said that quite frankly that he couldn’t see why anybody would want to search that way or read an article or book chapter that way.  He didn’t see as important.  That was about a year ago.  I was gracious and said that I don’t think that way of searching and reading is for everyone but I see it as a large growth area and I know we would eventually get people asking about it.  

Well guess what Mr. Sales rep, the college students of today are my residents and staff physicians of tomorrow.  They are also the current users of your products in college libraries NOW.  Their mobile web usage has jumped tremendously and you along with the libraries are missing out.  If my users don’t usage statistics on your resources drop below a certain line, guess what we drop your resources.  If people aren’t accessing your resources that I subscribe to because they aren’t mobile friendly and they are using the mobile devices, your usage statistics will drop.  How far?  Is it below that magic dropping line?  I don’t know but usage won’t grow, and you and I both want usage to grow.

Just to be fair, NLM’s PubMed smart phone app isn’t burning up the 3G networks either.  Just today, Wouter Stomp MD and Nick Genes MD, PhD who reviewed the 6 of best PubMed apps for iPhone and iPad for iMedicalApps.com said, “Although Pubmed has a mobile version of its website, it looks outdated and is not the easiest to use.”  So just because a library or vendor creates an app or mobile interface doesn’t mean that rest easy.  They need to find out how users use it and what other competitors or libraries are doing to improve their product. 

Are we starting to feel that we are missing the users?  I don’t know, I would guess it depends on your users and your library technology.  But I don’t think this mobile web access is a passing fad.  I think librarians, libraries, and library resource providers are behind the curve on this.

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3 comments - What do you think?  Posted by KraftyLibrarian - January 27, 2011 at 12:12 pm

Categories: Electronic Access, Journals and Books, Medline, SmartPhones, Technology   Tags:

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