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 That has been replaced by a link at the bottom of the citation indicating full text ability.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?

Labels: Medline Database, 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."

• South Central Region - Done earlier this month


• MidContinental Region - Done January 28th


• MidAtlantic Region - February 11th


• Pacific Northwest Region - March 25th (hopefully changes will be live)


• Pacific Southwest Region - Done, more scheduled when changes are live

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.

Labels: Medline Database, 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.

Labels: Medline Database, PubMed

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

Labels: Medline Database, PubMed

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.

Labels: Medline Database, PubMed

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.

Labels: Medline Database, PubMed, Technology

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.

Labels: Medline Database, PubMed, Technology

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.

Labels: ContinuingEducation, Medline Database, NLM, PubMed

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."

Labels: ContinuingEducation, Medline Database, NLM, PubMed

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.

Labels: ContinuingEducation, Medline Database, PubMed

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.

Labels: Medline Database, PubMed

"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

Labels: Medline Database, PubMed