Tuesday, March 31, 2009

Changes to PubMed SOON

There are going to be some big changes to PubMed happening very soon. Actually some of the changes are happening already. They are going live with changes as they come about. In January I blogged about some upcoming changes and the updates that many of the NN/LM regions scheduled to help inform us of the new look and searching methods.

For those of you who missed the updates, the MidContinental Region (MCR) has a recording of one of their sessions at https://webmeeting.nih.gov/p67806081/
For people who need a good video for patrons to show them the changes and how to search PubMed, check out Melissa Rethlefsen's tutorial at Mayo Clinic. http://liblog.mayo.edu/2009/03/04/pubmed-advanced-search-an-introduction/

Some of the big changes:

  • The Single Citation Matcher will be gone! -They are no longer maintaining this link and it will go away in the future. You can do a citation search right within PubMed's search box and it will realize that you are looking for a citation and display the citations of up to three articles in a light yellow box that appears above the search results..
  • The tabs (Limit, Preview/Index, Clipboard, History, etc.) will be gone. These functions will be available on Advanced Search.
  • Full text icons are already gone. Remember the little icon of a green page (indicating free full text)? That has been replaced by a link at the bottom of the citation indicating full text ability.
  • Term Young Adult has been added as an age term for articles 2009 onward. This term represents 19-24 year olds and will be available as an age limit when more articles are added that fit within this limit.
  • Citation display is slightly different. The title is now displayed first instead of the authors.
  • Gene Senors. Operates similar to the new Citation Sensor. The example the MCR used was braC1. When that is typed into the search box, it displays gene information in a yellow box just above the citations results.
  • The Drug Sensor detects whether a drug name is present in your search, and if it detects the drug then it gives information from the NCBI bookshelf. But don't get too excited about this sensor because it currently only detects about 200 drug names. MCR's example was lovastatin, if you type that in you will notice lovastatin results on the right hand side of the search page.
  • The Patient Sensor provides patient level information for drugs on the right hand side of the search page, title Patient Drug Information and is from 2 million citations
  • Automatic Term Mapping (ATM) -Basically this is just Googlizing the search process. PubMed used to have a specific search process for mapping search terms. It went first to MeSH and if it found a MeSH term then it would stop. The ATM still searches the terms as a MeSH but then also searches for the term in All Fields and if it is a multiple word term such as gene therapy, it will break up the term and search each word in All Fields. Personally that is a big pain in the neck and another reason why I am sticking with Ovid Medline.
  • My NCBI will have changes. You can change your password and email. Additional highlighting features have been added. PubMed Preferences will be where you turn on your filters for full text and free full text results (as well as other typical limits such as English and Humans).
  • My Bibliography is meant for authors to bring all of their publications into one place. You can only create one bibliography and is really only meant to be a save citation search place. It isn't meant to work with or as a citation manager.

In summary, Advanced Search is the way librarians are going to want to search. Librarians should bookmark this page. Librarians will have to determine what page they want their patrons to use and select that one for their recommended links.

There are a lot of other changes happening and unfortunately after watching the webinar, I have more questions regarding the changes rather than answers.

My questions and thoughts:
  • For institutions that don't use filters but use a special URL to show their holdings, how will the institutional icons be displayed in this new style.
  • I am not a big fan of Automatic Term Mapping (ATM). It just makes a big mess and adds way more citations to the results than you really need to deal with. But since we are in a Google world and people expect Google results, I guess we are stuck with ATM.
  • I am not quite sure why My Bibliography is useful. Most authors would want to have more than one bibliography and they would want something that works with or as a citation manager. Perhaps I am missing why this is an enhancement.

Why doesn't PubMed create the changes and show us the new version AHEAD of time while simultaneously running the old version? That way we can get used to it and test it ahead of time? That would make sense. Ovid did it with OvidSP, Ebsco did it with their new version. It isn't that hard and it gives users time to figure out the changes BEFORE they officially go live. Remember when the institutional icons displayed at the bottom of citations? That whole uproar could have been prevented if they had beta trialed it first along side the old version. It boggles my mind that we are supposed to imagine the changes that will be coming and we don't get to try them out before hand. I think is an unprofessional way to do updates and I don't know why PubMed does this. The librarian community would scream to heaven and hell if Ovid or Ebsco just all of a sudden made changes without first showing and offering the beta version first. Just because PubMed is free doesn't mean they shouldn't be held to many of the same operating standards as the pay database companies.

Anybody have any more changes to add or answers to some of the questions I have?

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Thursday, January 29, 2009

Recent and Upcoming Changes in PubMed

Your PubMed will be changing and getting a new look. Nicole Dittmar over at the eagle dawg blog links to Kay Deeney's (National Network of Libraries of Medicine, Pacific Southwest Region) question & answer session about recent and upcoming changes in PubMed. Many of the questions revolve around the Single Citation Matcher and MeSH.

According to Kay, "We don’t know when the PubMed home page will change; Single Citation Matcher and the Features Bar will disappear. We will plan on presenting more sessions reviewing the changes at that time." Thankfully Nicole has posted the dates for these sessions on her blog.


"Most of the NN/LM regions have already or are soon scheduled to give PubMed updates via free web conferencing."


Whether you are big PubMed or an Ovid Medline user it would probably be a good idea to attend one of these web conferences.


As Nikki mentions in another post, the official method of communication for feedback to the National Library of Medicine (NLM) about PubMed is to 'Write to the Help Desk' at the bottom of each PubMed page or via email to custserv@nlm.nih.gov. While this method is helpful for NLM to track data, it isn't too helpful to users or librarians because this "format doesn't allow for others to see what insights and challenges their colleagues are having."

One way for users and librarians to share PubMed thoughts and problems is to Twitter about them. People who already have a Twitter account merely add #pubmed to their tweet so that people can follow the PubMed discussion on http://search.twitter.com/search?q=%23pubmed.


I really enjoy the eagle dawg blog, she often has good stuff on PubMed as well as what is new at the National Network of Libraries of Medicine. It will be interesting to see how the #pubmed endeavor works out.

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Thursday, January 22, 2009

Rethinking Universal Searching

I was never a fan of universal search engines, after all I am a librarian and according to my husband anyway, I think differently. I find using MeSH and other controlled vocabulary systems to be extremely powerful when searching medical databases. I get frustrated and annoyed by various medical database vendors' universal searching, natural language searching, or basic keyword searching. After all, the medical databases I search were built upon controlled vocabulary and hierarchical subject headings and trees. I am fluent in MeSH, CINAHL, and EMTREE. Indeed searching these databases using the controlled vocabulary is almost like using another language. And there in lies the problem.


Regular searchers don't speak MeSH. For example: Until recently (2008) "cerebrovascular accident" was MeSH speak for "stroke." The term "pediatrics" refers to the medical specialty concerned with maintaining health and providing medical care to children from birth to adolescence, NOT the age group. These are just a few of the many examples of how the MeSH controlled vocabulary is not something regular library users would know.

Many medical databases vendors have built their systems to adjust for this. Many use some form of automatic term mapping to either force the searcher to choose a MeSH term or in the case of PubMed it automatically chooses terms and searches keywords unbeknownst to the user. Sometimes this process works very well for the user, other times the user scratches their head trying to figure out why "the stupid thing keeps spitting out more terms on a new screen."

Gone are the days when the librarian was the medical database and information gatekeeper. Doctors, nurses, and patients are hopping on the Internet searching for answers. Usually they come to the library when they want something beyond what they find on the Internet. They may want results that are beyond normal Internet results, yet they want the search process to be similar to Internet search or Google searching. Many of our medical databases aren't naturally set up for that kind of searching, that is why many of the vendors started adding universal searching, natural language searching, or basic keyword searching. Not surprisingly this created two different types of searchers that database providers must try to please, the expert searcher (medical librarian), and the basic searcher (normal people).

As a medical librarian I would tell you that I never use universal searching, natural language searching or basic keyword searching. Of course that would be a big, fat, red lie. I love Google almost as much as I love MEDLINE (remember my husband did say I think differently than normal people) and I use both almost equally. I use Google to search for things that are particular stumpers in MEDLINE. Often it starts my brain thinking in a different direction and I apply that to a new MEDLINE search which might yield different or better results.

I also use Google to search for non medical resources, and it is during these times that I am most like the average searcher. I am searching something very similar to a universal search engine to find information on subjects which I am not an expert searcher. Sometimes I am looking for an odd news article and while another journalism, public, or academic librarian may know the exact news database that indexes that specific paper, I don't and I don't necessarily have access to it. So I use Google. Other typical Google searches could be on home repair, business information, investments, minor questions about the law, etc. It is at these times that I can understand the easy searching appeal universal searching has for normal library users searching for medical information.

As I mentioned, more and more database producers are creating "simpler" search features for the average person. Libraries are also adding universal searching on their web pages or on their catalogs. For example: OhioLINK's front page features a universal search to find "a few good articles and books." Library users can search the "Next Generation Melvyl" at UCLA Library, a universal search engine that finds articles, books and many more resources. The University of Iowa Libraries' "Smart Search" will not only find books and article but it will also find images in their digital collections including the Hardin MD Gallery Collections.

Christopher Cox said, "boundaries are being blurred between the academic and commercial Web, between library resources, between the citation and the item itself. Students have no patience with these arbitrary boundaries; they want information, and they want it now, wherever it may be located." (An Analysis of the Impact of Federated Search Products on Library Instruction Using the ACRL Standards, portal: Libraries and the Academy. 6(3), July 2006, pp. 253-267.) Libraries users want and use universal searching, librarians need to adapt to provide other methods to help users to search for information rather than freaking out that their beloved database product now has a universal search, natural language search, or basic keyword search feature. Perhaps our education efforts should slowly be changing from always teaching the proper MeSH search strategies to how to find good information fast and to know when you to ask for help when you need more.

I tease my husband that he took the dead language Latin in high school, however what will MeSH and other controlled vocabularies be years from now? Only learned expert searchers seem to be the ones still fluent in MeSH speak, the average person is not. Latin didn't really die, it just evolved into other languages. Our language for searching is evolving too.

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Tuesday, December 23, 2008

PubMed Year End Processing

NLM finished the Year End Processing December 15th. The NLM Catalog, MeSH database, and translation tables were updated to reflect 2009 MeSH and the information is now current. Important to note, the Index to the NLM Classification will not reflect 2009 MeSH changes until Spring 2009.

Here are some other changes you might be interested in:

  • NLM Bibliographic records will now include three new Publication Types; Cookbooks, Formularies, and Poetry.
  • NLM implemented the new PCC (Program for Cooperative Cataloging) Guidelines for field 440 (i.e., use 490/830 in lieu of 440) beginning November 24, 2008.
  • NLM will now copy tables of contents (TOC) and summary notes available from the Library of Congress 856 links into the bibliographic records.

Go to the NLM Technical Bulletin for more information on these changes and links to many others.

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Monday, December 15, 2008

Why Do They Keep Changing PubMed?

I feel like this month is flying by and that I am constantly treading water to stay a float. It is a busy time for me personally and professionally so unfortunately this blog hasn't been updated as much as I would like it to be. If you like reading it, don't worry, I am not getting bored with blogging. I just don't have the time right now, which frustrates me because I think blogging allows me to get some of my ideas out into the open. I will do my best to keep posting regularly and hopefully after the holidays I will be able to get on a consistant posting schedule again.

Thankfully, the Eagle Dawg blog has taken up the slack and she has posted a very interesting post titled, PubMed and the Discovery Initiative discussing some of the changes happening with PubMed.

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Thursday, November 20, 2008

MeSH for 2009

Happy New Year a little early to all of you MeSH heads. The NLM Technical Bulletin has published the 2009 changes and additions to MeSH. Don't forget to check your SDIs, your saved MyNCBI searches, and any other ongoing searches that may have some vocabulary changes that might effect the outcome of your search.

Here are the list of descriptor changes:
New Descriptors - 2009
Changed Descriptors - 2009
Deleted Descriptors - 2009
New Descriptors by Tree Subcategory - 2009

If you are interested in how things sit within the Tree, there were some major changes related to fungi, disciplines, and occupations.

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Friday, November 14, 2008

PubMed Advanced and PubMed Basic Changes

According to the NLM Technical Bulletin, the PubMed Advanced Search soon will no longer be in beta. It will be the place for people to do field searching, limits, and other features.

IMPORTANT: In the near future the tabs for Limits, History, Preview/Index, History, Clipboard and Details will be REMOVED from the basic PubMed search pages.

I don't think I am going to be a big fan of tab removal "improvement."

For more information on the changes go to http://www.nlm.nih.gov/pubs/techbull/nd08/nd08_pm_adv_search_evolves.html

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Wednesday, October 15, 2008

Review of OvidSP Platform

Marie Fitzsimmons and Valerie Gross recently published an interesting article in Medical Reference Services Quarterly, A Review of the OvidSP Platform. (2008. v.27 (4) 394-405 DOI: 10.1080/02763860802368142)



Abstract:
As part of its mission to advance the technological capabilities of its products, Ovid introduced a redesign of its database platform in fall 2007. The platform redesign brought new features and enhancements to an already robust system. The transition between Ovid Gateway and the OvidSP platform was orchestrated seamlessly. With the OvidSP platform came innovative changes such as the incorporation of Natural Language Processing associated with the new Basic Search mode. Discussed are OvidSP features, advantages and disadvantages of the new platform, customizable settings, and future direction.

The article discusses OvidSP Advanced, OvidSP Basic (Natural Language Processing), and the advantages and disadvantages of the new platform. The article was received June 13, 2008, a pretty good publishing turn around time for an article in Haworth Press, however it is important to note that Ovid has done at least one update since the article was written.

Ovid has made some serious investment in the SP platform so I think we will see some interesting features and improvements to the platform in the future. One thing I hope they will consider doing sooner rather than later is to allow people to email citations in HTML. That is a crucial feature when dealing with research, full text articles and links. You cannot provide one stop shopping research services if you patrons have to open up two windows (your A-Z list of online journals and their email with Ovid citations) to find and download the full text of an article.

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Tuesday, October 07, 2008

My NCBI Changes and PubMed's ATM Goofs

If you are big PubMed user you probably already know that My NCBI has changed. The biggest change you will notice upon login is the display. The My NCBI homepage for your account displays your preferences, filters, saved searches, collections and bibliography.

My Bibliography is new. It is designed to "make it easier for authors to search and collection citations for their publications." Using a template, an author can create a saved search and when it is updated the new citations are added to the bibliography. The search strategies are based on either an author's name or a list of PMIDs. Each bibliography can hold up to 1500 citations.
To learn more about these and other My NCBI changes go to : McGhee M. Coming Soon to My NCBI: New Features, New Navigation, and My Bibliography. In the NLM Technical Bulletin.

The bibliography feature is interesting. I am curious to see how it will be used, especially how those who use RefMan, EndNote, or Refworks might use it.

While some PubMed changes like My NCBI were a little more obvious to the naked eye, there were other things happening that you may not be aware of. A few months ago the folks at PubMed poked a stick at the hornet's nest by implementing Automatic Term Mapping (ATM). Well there have been some changes with that as well as citation censor. I heard about these changes from a librarian with the GMR while I was at the Ohio Health Sciences Library Association meeting Friday.

ATM has changed. For example if you type in the term multiple sclerosis then click on the Details tab you will see:
"multiple sclerosis"[MeSH Terms] OR ("multiple"[All Fields] AND "sclerosis"[All
Fields]) OR "multiple sclerosis"[All Fields]

Notice how multiple sclerosis is split apart and you are searching for any article where multiple can be found in any field with any article where sclerosis is found in any field.

In previous examples they use factor b as a search term to illustrate that it won't be split up like multiple sclerosis. However, when I did a search in PubMed typing brain ct in the search box I got four results, so I clicked on the Details tab I saw this:
brain ct[Author]

Hmm, not what I would normally want if I was searching brain ct. You have to type "brain ct" with the quotation marks for it to search it in all fields and to treat it as one word. Of course using quotations prevents PubMed from searching MeSH as you can see if you type "multiple sclerosis" in the search box and click Details.

What normal searcher is going to type brain ct in the search box and expect to get the four articles by Dr. C. T. Brain (yes there is one) instead of articles on Brain Computed Tomography!??

The folks in charge of PubMed want it to be more user friendly, I certainly don't see how that is user friendly. I absolutely LOVE Ovid's mapping. When I searched for brain ct, Ovid's mapping was at least smart enough to map me to something appropriate, it did not try and connect me with Dr. Brain's articles which have nothing to do with computer tomography what so ever.

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Wednesday, August 27, 2008

PubMed Now Indexes Videos of Experiments and Protocols in Life Sciences

I read an interesting little article today in The Chronicle of Higher Education, PubMed Now Indexes Videos of Experiments and Protocols in Life Sciences. The Journal of Visualized Experiments is now indexed in PubMed.

Journal of Visualized Experiments (JoVE) is a peer reviewed, open access, online journal dedicated to the publication of biological research in a video format. JoVE states, "Visualization greatly facilitates the understanding and efficient reproduction of both basic and complex experimental techniques, thereby addressing two of the biggest challenges faced by today’s life science research community: i) low transparency and poor reproducibility of biological experiments and ii) time and labor-intensive nature of learning new experimental techniques." Recently JoVE an agreement with various science publishing companies such as Current Protocols for joint protocol publication. This video on the "Preparation and Fractionation of Xenopus Laevis Egg Extracts" was jointly published by JoVE and Current Protocols.

According to JoVE's official blog it is "first video-journal to be accepted in PubMed." Well that is probably because JoVE is a unique journal. I don't see that many peer reviewed protocol video journals out there. Don't get me wrong, it is good that they are indexed in PubMed and that helps speak to their content and their credibility, but it their videos aren't the only ones to be indexed in PubMed. There are now quite a few videos from index journals that show up in PubMed. For example you can find the citation to the video "Placement of a Femoral Venous Catheter" by Janet Y. Tsui in the New England Journal of Medicine. The indexing of the videos shows NLMs commitment to medical information beyond the printed word.

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Friday, August 15, 2008

Ovid Updates

I am sure some you loyal Ovid users have already noticed the most recent update that went live yesterday (August 14, 2008). Ovid's enhancements will be delivered in two phases, workflow improvement (first) and new features (second). This most recent update was to fix a lot of the workflow and interface issues that many have been bugging Ovid about.

So here are the updates:
  • Search Tab Additions and Enhancements - New Multi Field Search Tab which according to Ovid it will "allow for a more targeted and specific search experience." Basically this tab reminds of searching in EBSCO, it allows you to easily search for multiple things within multiple fields all at one time.
  • Seach Aid Box is collapsible
  • Results Manager Box is collapsible and is available above and below the search results.
  • Search History Box can be moved either above or below the green Search Box.
  • Limits can be customized to display on the main search page.
  • Ability to create, edit, and add multiple annotations to a citation. (You must be logged into your personal account section for this to work.)
  • Browse Books and Browse Journals links are now on the Select a Database page
  • Font size is now adjustable from your browser
  • Users logged into their personal account area will now see their name and institution.

Coming Soon:

  • My Projects - a workspace area for saving and managing files
  • Ovid Universal Search - a cross platform search solution

I am happy with the new release. Heck I am just happy that the jumping screen was fixed. But the improvements on this new release are nice. However I have got to wonder why Ovid still clings to that Results Manager Box. Many other databases have a much nicer method for saving results. I especially like EBSCO's method. The reason I like it is that is clear and simple. It resembles how many Internet commerce sites allow you to shop and easily add things to the basket. In my opinion the Ovid Results Manager is confusing to regular patrons and it takes up space, they should go to the add to basket approach.

Enhancements I would like to see:

  • Cited References - MUST have the ability to add the cited references from a citation to your search results. I don't know why this ability was in place when searchers were given the ability to look at cited references. I would think this is an important feature. I know a lot of researchers who routinely look at the cited references for article.
  • HTML Email – This is another MUST HAVE improvement that is long overdue. Currently librarians or regular users are only able to email the search as a text file. That means all of the full text links to the articles are gone. People no longer want the citations just emailed to them, they want to view the full text of the article to the citation they like. Therefore you need to have the ability to send the email in HTML and preserve the full text links. PubMed already does this and frankly I don’t know why Ovid doesn’t.
  • Search Box For Journal Browser – How time consuming is it click J then click Next a bunch of times to finally get to the listing for the Journal of the Royal College of Physicians of London. A search box would speed up and make the Browse Journal process so much better.
  • Sharing Notes – I think it would be neat if two researchers working on the same topic could view each other’s retrieved searches and have the ability to include their personal account notes they made on the citations. I am not sure how that would work and whether Ovid’s My Workspace enhancement would do this, but I think it would be a cool enhancement.

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Monday, August 04, 2008

PubMed Instruction: Classroom vs. Online Instruction

I meant to blog about this earlier when I made the post about the reviw of Zotero, Skype, and PBWiki, but I got side tracked. So better late than never.


Do you teach a lot of PubMed classes? If so you might be interested in the recent article, Measuring Medical Student Preference: A Comparison of Classroom Versus Online Instruction for Teaching Pubmed published in the Journal of the Medical Library Association. 2008 July; 96(3): 217–222. doi: 10.3163/1536-5050.96.3.007.

The author, Laura Schimming decided to compare medical students' satisfaction with PubMed instruction taught in the classroom with an online tutorial. She found that students were more satisfied with online tutorials and the students who took the online tutorial passed the PubMed skills assessment at the same high rate as students who learned PubMed in the classroom.
I think it is interesting to know that the librarian used Dreamweaver instead of Camtasia or Captivate to create the online tutorial. The online tutorial was a split screen tutorial where the instructions and information was at the top and PubMed was below. This allowed users to read the information while actually practicing on a live PubMed session. It truly was more of a hands on tutorial.
So what does this mean for librarians who teach PubMed? I think it gives librarians more options and flexibility. Having an online tutorial for students to use can free up the librarian to teach other classes that may not lend themselves as easily to an online tutorial format. It also allows students to take the online class on their own time. An additional benefit is that unlike a traditional classroom the tutorial is available to use again should they need a refresher. No wonder the students preferred the online method.

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Friday, July 18, 2008

PubMed Search Clinic Video Available

The video from yesterday's PubMed Search Clinic is now available at http://www.nlm.nih.gov/bsd/disted/clinics/pmupdate08.html so if you missed it you can still learn about the changes.

The presentation covers the changes made to PubMed including: automatic term mapping, citation sensor, and advanced search page.

Citation Senor:
It is a new feature designed for users seeking specific citations. Simply put the citation information into the search box and click Go. The Citation Sensor looks at that information and if it looks like it is citation information it will try and find matches. It will display the matches in a yellow box.

I see this as handy, but I have to say I really like the regular Citation Matcher that is listed on the left hand side (in the blue bar) of the front page. I like it because quite often people have the wrong spelling, wrong journal, wrong year when looking for a specific citation. I think the Citation Matcher makes it easier to account and adjust for these errors. For example, it suggests author and journal titles. There are a lot of ways to misspell Tchorzewski, however if you are close and at least type in Tch, PubMed will at least suggest the rest. You don't get that with Citation Sensor. But who knows maybe Citation Sensor will grow on me.

Automatic Term Mapping (ATM):
PubMed has had automatic term mapping for quite a while, they just have made some recent changes. The old ATM mapped search terms to subject, journal, and author tables in a certain order. If a match was found in the MeSH table it would stop mapping, it wouldn't search the author or journal tables. According to NLM this was frustrating to users. The new ATM still does check the original fields (subject, journal, author) in the same order but it also now checks all fields for phrase and individual terms.

July 2, 2008 changes to ATM:
Based on user feedback, they made some enhancements to ATM. Substance names (known as MeSH supplement or concepts) and MeSH with stand alone letters or numbers will not be broken apart and searched. They will be searched as a phrase. For example: "factor b" will not be split up.

The new ATM changes mean that users will retrieve more results. They found that searches retrieved on average 10% more citations. NLM has provided an FAQ for more information and reasoning for the new ATM.

Personally, I still don't like PubMed's searching and mapping features. I really really like the way Ovid maps and suggests terms. It almost forces keyword searchers to think about using MeSH terms. PubMed doesn't do that, people enter terms and are blindly mapped to terms and keywords. Yes, they can click the Details tab to see what it is doing, but how many users do that? Getting PubMed to search MeSH terms is better than it has been in the past but I still think it is clunky.

Advanced Search:
The beta for Advanced Search was launched on May 15, 2008. The screen has four collapsable sections allowing you to shrink or expand various sections as needed. The search box and the History are at the top, History works the same as previously. The Search by Field section is next and the default fields displayed are Author, Journal, and Publication Date which are the most commonly searched. However, you can search by other fields as well. Just right of the search fields input box there is an odd little icon/button that gives you access to the index for the selected field. The Limit section is the next section on the page and you can carry your limits to future searches using the lock icon (defaulted to carry your limits to future searches). Finally, there is the Index of Fields and Field Values box. This feature is helpful if you want to add multiple items from one specific index.

If after viewing the clinic, you still have some general PubMed suggestions you should consider sending an email to their customer service which you can find on the bottom of most NLM pages as Write to the Help Desk. The instructors feel that the PubMed improvements have helped with searching. If it hasn't they want your feedback with real searches and real examples.

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Wednesday, July 16, 2008

Don't Forget PubMed Search Clinic

Nikki (Eagle Dawg Blog) has posted a guest post on David Rothman's site reminding us all about the 30 min. PubMed search clinic offered tomorrow July 17 at 2pm Eastern time.

Don't forget the class is only open to the first 300 participants to login. If you get shut out or you can't otherwise make it at that time, never fear, the session will be recorded and available for viewing at a later time.

Do you have questions for the search clinic? Unfortunately they will not be able to take questions using audio. Please use the Chat (Q&A) pod to type questions and comments to the trainers. Feel free to enter your questions throughout the presentation.

Nikki also reminds us of the technical requirements for participating in the class. "If you have not used Adobe Connect before (or since they acquired Macromedia Breeze), check that you have the most recent free Adobe Flash update (version 9.0.124) as using 9.0.115 and earlier versions may result in audio problems while accessing the archive later on. I recommend viewing the recent ‘Awakening the Searcher Within’ seminar series from the National Network of Libraries of Medicine, Pacific Northwest Region (NN/LM PNR) archive both as a way to test your audio and see how the chat pod is used in Adobe Connect in addition to reviewing some great search strategies."

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Thursday, July 03, 2008

Online Search Clinic From NLM Regarding PubMed Changes

There has been a lot of chatter recently regarding some of the changes in PubMed. While I have been kicking the tires and testing out CINAHL in EBSCO 2.0, others have been detailing some of the changes happening within PubMed. Now the National Library of Medicine will be conducting a 30 minute online search clinic on July 17, 2008 at 2:00 eastern regarding the PubMed changes. The presentation will cover how PubMed handles your search with the Automatic Term Mapping (ATM), Citation Sensor, and Advance Search beta.

For more information and access to the meeting, go to: http://www.nlm.nih.gov/bsd/disted/clinics/pmupdate08.html.
Due to technical limitations, there is a maximum capacity of 300 participants.
The clinic will be recorded and available for viewing at this address. Comments and suggestions regarding the search clinic are welcome.

Personally I think this is a must see for medical librarians, but is especially important for medical librarians who rely primarily on PubMed for MEDLINE searching.

If you are interested in reading what others are saying about the changes Laika, Keith Nockels, and Eagle Dawg all have fairly recent posts on the new PubMed features. It might be a nice way to quickly familiarize yourself with the issues before NLM's presentation. Perhaps their insights might cause you to generate some interesting and thought provoking questions, comments, and suggestions that you would like to submit to NLM prior to the clinic on July, 17th.

In Laika's MedLibLog post, PubMed: Past, Present And Future, PART II she describes some of the changes and enhancements that NLM has implemented in the PubMed interface. She has a very in depth description and analysis of PubMed's "most recent, most radical, and yet most poorly announce change," Automatic Term Mapping (ATM). She illustrates her thoughts using several search examples and how PubMed handles them using ATM. She investigates new features such as the Citation Sensor, Advanced Search Beta, and some other minor changes.

She discusses the majority of changes in Part II of the series. Part I discusses past features and tools within PubMed and the need to make them easier. Part III discusses the possible future of PubMed and what she would like to see occur.

Keith Nockels over at Browsing posted, Changes to PubMed where he lists what changes he will discuss with the departments to which he is a liaison. He briefly discusses the missing sidebar, Advanced Search, ATM, Citation Sensor, Title Sort, and a new spellchecker.

Eagle Dawg's Blog post, New ATM & PubMed: Straight to the source is an update from her brief PubMed Review shoutout (MLA 08) which has a direct link to the 25-minute PubMed Review slides & audio presentation. She lists the three "must see" sections of the video as the Advanced Search Beta, ATM, and Using Advanced Search to focus subjects due to ATM. Eagle Dawg also provides al ink to NN/LM PNR's blog entry which is a brief tutorial on the changes.

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Wednesday, July 02, 2008

Updates for OvidSP

On July 31, 2008 Ovid users might notice a few new changes. According to Ovid "this release moves beyond traditional searching, delivering enhancements and exciting new functionality that improve search flexibility, personalization, and sharing capabilities, so that users can work the way they want to work."

These new features will be:
  • The main search screen will be streamlined with a sleeker and more intuitive design.
  • Search Tab Addition and Enhancements - A new Multi - Field Search tab will allow for a more targeted and specific search by providing multiple search boxes for assigning specific fields. (I have no idea what that means but will see how that works)
  • User Workflow Tools - The Search Aids box will be collapsible. Results Manager and Search History will be moveable. Font size will be adjustable via the Internet browser, and annotations will be enhanced. Email capabilities will be expanded (they dont' say how).
  • My Project Workspace Area - This is a new feature and is a direct result from customer feedback. The My Projects will provide a workspace for assemblind and organizing research findings for easier management and it is linkable from every page in the application.
  • Universal Search - This is a new "premium search offering" and is available as an add-on. It will deliver cross platform content searching within the OvidSP interface.

Ovid recomends the OvidSP Resource Center to find information on the upcoming release. In the next few weeks Ovid will add new training schedules, tutorials, and screen shots.

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Monday, June 30, 2008

Thougts on EBSCO 2.0

I really like the look and feel of EBSCO 2.0. Here is a brief run down of the new features you will find in EBSCO 2.0.



REMEMBER: EBSCO 2.0 will go live sometime in July!


Please note: I have only been testing CINAHL in EBSCO 2.0. My original test search was Caffeine and Arrhythmia. I did a few different methods of searching. I searched using subject headings, text words, and the combining terms using the search history.

Search Results: They are displayed in the middle of the screen. Quick methods to narrow the results further are display in two frames on either side of the middle screen. The nice thing is that these side screens can be collapsed providing more screen space to view the results in the main center screen. On the left hand frame, users have the option to limit their results by Source Type, Subject, Subject Major Heading, Age, Gender, and Publication Type. I am a little confused as to the difference between Publication Type (which only has book chapter) and Source Type (which has Periodicals, Book/Monographs, and CEUs). Why have both, why aren't they all under one "type," either Source Type or Publication Type?



You can click on the small arrow on the frame border to collapse or expand (once collapsed) the frame. In order to see how the left hand frame performed I just searched for Arrhythmias as a subject term. I then narrowed my search down using only the options provided on the left hand frame. I was able to easily narrow it further to Females, 65+, and Heart Failure, Congestive. EBSCO 2.0 provides a link to more subject headings from the left frame. For example, Heart Failure Congestive was not listed as a subject on the left hand frame but I just clicked More and EBSCO 2.0 provided me with a list of a few more possible subject terms. Just like in the older version of EBSCO, if users have narrowed themselves too far by using the left hand frame, they can click on the breadcrumb links up at the top of the results to broaden the search again. However, in 2.0 users can now remove items from the breadcrumb trail by clicking on the "x" and if they want, users can start a whole new search using any of the terms listed in the breadcrumbs.



In the 2.0 version the right hand frame allows people to limit results to full text and references available. It is also the area where items in the save folder are displayed. I think this is a nice feature that allows you to see at a glance the titles of articles you have saved. But if it is distracting or takes up too much screen space, users can click on the frame arrow and collapse it. Searchers can click on the Search Options link to see the entire limiting options within CINAHL. The main search screen grays out and the limit screen is super imposed on top allowing the searcher to quickly select the desired limits.

Searching Itself: From what I can tell not much has changed between 2.0 and regular EBSCO. I am not a big fan of EBSCO's search interface. I think the confusion and problems come when users try and search using the Subject Terms. We have the default checked to automatically suggest subject terms because we think using subject terms in the medical databases (such as CINAHL) is a better way to start off searching. When searchers type in a term like arrhythmia it maps to suggested subject headings. Here is where it gets confusing. The searcher selects the term then must look up at the top and click Search Database. It is extremely easy to accidentally click Browse, I have done it myself quite a few times. Clicking Browse just retrieves and displays the same set of subject headings. To librarians we usually know we clicked the wrong button, to regular users it appears they just caught in a loop.

Search History: If a user has multiple searches and wants to combine them together, they will want to click on the Search History link which located just above the search results (similar location to where the Search History tab is in regular EBSCO). This is another area that still could use some improvement and can be confusing to users. EBSCO keeps the current search in the search box and it is still present in the box when users click on Search History. The user must delete the search strategy left in the search box when they are checking searches they wish to combine. If they don't, the checked boxes are combined with the left over search strategy causing some confusing results.

Viewing Search Results within Search History: In regular EBSCO when users clicked on view search results it exited the Search History area and displayed the results. In EBSCO 2.0 it stays within the Search History and displays the results below the Search History. This can be confusing because unless users pay attention they might just think they are caught in a loop constantly viewing the Search History. It is not immediately obvious that they must scroll down to view the results.



Viewing Search Results in general: The citation display in 2.0 seems to be a little easier to read and has a slightly cleaner look than regular EBSCO. I think this because citation's title is displayed on one line while the rest of the citation information is displayed below. It also appears that the title is in a slightly larger font than the rest of the citation. For the most part I never had any problems with regular EBSCO's citation display, but this seems to be nice subtle improvement.

My absolute favorite feature improvement is the ability to hover over the magnifying glass to see the abstract while still viewing the list of citation results. No more clicking the title to see the abstract then clicking again to get back to the results list. Simply hover over the magnifying glass next to each citation and a bubble pops up with the abstract, then if the searcher is interested in the full text they can click on the buttons within the bubble to add it to the folder or view the PDF.



Easier Bookmarking: In regular EBSCO searchers could see the persistent URL at the bottom of the citation but now EBSCO 2.0 makes it easier bookmark citations by providing direct linking to a whole slew of bookmarking services such as del.ici.ous, furl, digg, etc. Articles, searches and publications can all be bookmarked.



Other features: The following features are not yet available in CINAHL and MEDLINE or are not as noticeable.



Image Quick View (IQV) - The thumbnail of the image(s) in articles can be found below the citation on the results list. These images can be pictures, illustrations, charts, and graphs. However, this option is only available with EBSCOhost journals with native PDF. All other full text journal articles with images will not have not IQV. While this is a nice way to handle images, I found that there just weren't a lot of results within CINAHL that included the IQV.



Date Slider: The date slider is not yet available for MEDLINE or CINAHL. When it is available it will be located in the frame on the right hand side. I tried using it in Academic Search Premier, it was ok, but I found it a lot easier just to type in the limiting dates beneath slider bar rather than sliding it to the desired range.



SmartText: SmartText searching is not yet available for MEDLINE or CINAHL. It allows the searcher to search any text from any article or document. Users paste a sentence, phrase, paragraph, or entire pages into the search box and will retrieve a relevant result list. I am not sure how much medical librarians will need this type of search. Perhaps if we have bits and pieces of the article we would be able to find the exact article. I thought this might be helpful for teachers or librarians investigating student plagiarism. I decided to try this method of searching in Academic Search Premier. I selected SmartText from the Advanced Search options and then I cut and paste in the box the sentence, "Cardiologists from Chicago report the case of a healthy 23-year old woman who was brought to the emergency room because of palpitations (a feeling of her heart racing) and chest tightness shortly after she drank GNC Speed Shot and a Mountain Dew soft drink. Her heart rate was dangerously high, and the doctors had to give her a medication to reduce it to normal."

I got 158,566 results (full text, 2005-2008) and the original article with that text was not listed as a top result, I couldn't find it, it was buried somewhere within those other articles. Over 100,000 citations is an awful lot to go through, especially when the simple search on caffeine produced a mere 821 citations (full text, 2005-2008). I am not so sure how SmartText is at all helpful to anybody.



Final Thoughts:

I like the overall look and feel of the new EBSCO 2.0. I think the display is cleaner and easier to navigate. I especially like hovering to view the abstract and the fact that bookmarking is easier.



I am still not a fan of EBSCO's search interface for medical or nursing searching. I think Ovid handles mapping much better and still has the best search interface (despite its quirks). If I could just attach Ovid's mapping and search interface with the rest of EBSCO 2.0's features and design, I would be a happy searching librarian.



I am confused as to how certain features like IQV, the Date Slider, SmartText would be helpful, relevant or needed by medical librarians searching the medical and nursing and allied health literature.

Don't forget to try EBSCO 2.0 out for yourself and read about the enhancements and changes. Tomorrow is July and EBSCO said it will release 2.0 sometime in July, so there is not much time left to play around before it goes live.

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Thursday, June 19, 2008

PubMed Frustrations

Yesterday PubMed went down. I am not a usual PubMed searcher. My MOC (Medline Of Choice) is Ovid, so I didn't notice the problem immediately. However, I began to field a number of calls from patrons regarding our full text journal links in PubMed not working. Two other librarians also started to notice some odd things occurring as well. Initially it appeared as if it was an issue specific to LinkOut and using Serials Solutions as the outside tool. Only after further investigation and a call to Serials Solutions support did we discover that it was a larger problem with PubMed. Apparently PubMed's servers went down at 1:00am that morning.


As usual the the emails started coming in from Medlib-l regarding PubMed. Librarians from different areas of the United States asking about the health status of PubMed as they too noticed it doing funky things. There was a brief discussion and some questions raised on Twitter Medlibs about what to do if PubMed goes down and you don't have access to Ovid. What do you do, where do you send patrons? Would third party tools work?

PubMed is free. PubMed is available to all. When it goes down, it is felt by a great many people. That is why it absolutely puzzles me to no end that PubMed can't even send out an email or post a note on their site that they are having difficulties. A simple note so that the various people around the world know that it is not their library, their institution, or their searching skills, that are causing the problem. Remember in order for us to find out it was a PubMed problem not our problem or our outside tool problem, a second party (in this case Serials Solutions) had to tell us. We are a medical library, we should be informed. We shouldn't have to find out from another company or ask other librarians via email whether it is working. There should be an obvious note on the site when there is an outage or if there are problems.

Yesterday, problems surfaced because of server malfunctions, an unplanned event. However, how many times has PubMed changed something internally and librarians were left scrambling to figure out why their settings changed, why their icons were no longer displaying, or other odd things? About 2 years ago at my previous job, I purposely held off activating the outside tool feature in PubMed for a while because at the time there were quite a few emails being sent regarding PubMed's problem handling of icons.

Just because PubMed is a free doesn't excuse their lack of communication. PubMed has become the premiere tool for many librarians, researchers, students, etc. to search the biomedical literature. They should notify their customers of outages.

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Wednesday, June 18, 2008

EBSCO 2.0 Beta Available

If you are an EBSCO customer you should know that EBSCO 2.0 is available in Beta to help users test drive and familiarize themselves with the new interface before it becomes official in July of 2008.


You can get to EBSCO 2.0 by clicking on the New Features links on the top right hand area EBSCOhost.


Here are some things you should know before you start to play with the new version.

  • Administrators will not have the ability to customize the interface settings during the EBSCOhost 2.0 BETA preview.
  • A few databases including the CINAHL and MEDLINE suites of databases will not have the date slider and SmartText Searching features available at the release of EBSCOhost 2.0. They do expect to have these features available on these databases soon.
  • Users are encouraged to try out the My EBSCOhost features in the EBSCOhost 2.0 BETA but current personal accounts will not be available.
  • Users are free to set up a new temporary account in the BETA version to store articles and set up alerts but any saved content will not be carried over to your current account. Additionally, any saved alerts will not run. When EBSCOhost 2.0 is released, your current My EBSCOhost account will work properly and your saved information will be available.
  • Because this BETA version is being hosted differently than the current EBSCOhost, users may experience some performance issues or possibly a temporary interruption as updates are made. This will not be the case when EBSCOhost 2.0 is released in July 2008.
  • Searches conducted in the preview site will not be logged in your institution's statistics.
If you don't have EBSCO but are still interested in the new features EBSCO 2.0 will have, you can go to EBSCO's Marketing site to view a Flash demo (10 min. run time, no audio), PowerPoint slides, descriptions of the new features and functionality, and a brochure.


Time for me to get in there and start kicking the tires. I love trying out new things.

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Thursday, June 05, 2008

PubMed Changes

"Have you noticed PubMed searches are retrieving more citations than you expected? Are stored My NCBI automatic updates including more than they did previously? Have you tried the beta version of Advanced Search in PubMed? NLM has introduced many new features to PubMed in recent weeks!" The Pacific Northwest Regional Medical Library news briefly describes PubMed's new automatic term mapping. The automatic term mapping now searching your term in All Fields which usually results in more retrieved citations. Of course this might also mean you will retreive more false hits as well.



Two other places you might look for information are:

NLM Technical Bulletin article -briefly describes automatic term mapping and includes images.

NLM’s presentation on PubMed - Webmeeting slides and audio from MLA 2008 Chicago

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Tuesday, June 12, 2007

PubMed on the Fritz

Previously I didn't post much about PubMed not working because in the past problems seemed to be few and far between and were resolved fairly quickly. But now, I don't know what is going on. All I can think is "Good Grief Charlie Brown." I don't think I a week has gone by these past couple of months that I haven't read some email about PubMed not working.

I have been slow to add my new library icons to PubMed because it just seems to be one big mess after another. I am all for the idea of perpetual beta but this is a little much. What is worse is that I think we librarians are left a little in the dark, wondering if it is our fault (icons, urls, etc.) or if it is PubMed's fault. There appears to be a big communication problem. Perhaps PubMed might have a updated blog or information page detailing the known issues and resolutions.

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Thursday, May 10, 2007

Teaching Medline to Medical Students

I am very excited, starting with the new incoming class of medical students I will be teaching three one hour classes on Medline to the medical students. I have noticed that many of medical students coming to us were fairly unfamiliar with Medline (either PubMed or Ovid) and were really struggling to do research. After some questions and some gentle probing I learned that the students were not taught Medline in their first two years at school because they weren't doing the type of research that warranted using Medline. In their third and fourth years the medical students began hospital rotations and were on the medical school campus less frequently. However, this was also the time where they are expected to do a lot more in depth research and writing. From what I could tell, there was no formal training on how to do research once students entered into their third and fourth years. I was teaching them one at a time whenever I could get a chance, fifteen minutes here, a half hour there. But there was no official time to teach them and I was only able to reach the students who sought help.

Well now I am added to the education schedule! Instead of 15 minutes here and there, I get three classes for an hour each class. While I am a very excited about this, I am going to have to sit down and figure out what I want to teach them. My method of teaching Medline to the students has been more akin to speed dating, try and reach as many people as quickly as possible to make a connection. While it is definitely not the best method for teaching, they rarely had time for anything else and at least it got my foot in the door for follow up questions.

I thought I would ask what you would do and teach in three one hour classes on how to do Medline. What are things you have learned that work well, that don't work well? what are some good search questions that illustrate certain aspects of searching Medline? What about mini pre and post test to see how much they have learned? The table is open for discussion, feel free to post your thoughts. We can all benefit from the sharing of ideas.

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Wednesday, February 21, 2007

BabelMesh and Txt2MEDLINE

Here are two new options for searching MEDLINE courtsey of NLM.

BabelMesh is a cross-language search to MEDLINE/PubMed. Users can search using single terms or complex phrases in Arabic, Chinese, English, French, German, Italian, Japanese, Portuguese, Russian, and Spanish. The citations and abstracts retrieved will still be in English only.
To search BabelMesh go to http://babelmesh.nlm.nih.gov/
For more information read:
Liu, F, Fontelo P, Ackerman MJ. BabelMeSH: Developmentof a Cross-Language Tool for MEDLINE/PubMed. 2006.

Txt2MEDLINE, in beta test, a text messaging system for processing incoming Short Message Service (SMS) queries, retrieving medical journal citations from MEDLINE/PubMed and sending them back to the user in the text message format.

To check out Txt2MEDLINE go to: http://sms.nlm.nih.gov/tbl/index3.php
For more information read:
Fontelo P, Liu, F, et al. Txt2MEDLINE:Text-Messaging Access to MEDLINE/PubMed. 2006

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The Krafty Librarian has been a medical librarian since 1998. She is currently the medical librarian for a hospital system in Ohio. You can email her at: