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Is Chocolate A Food? A Problem In PubMed

By Eric Rumsey and Janna Lawrence

As we’ve written, searching for food-related subjects in PubMed is difficult because of the way the MeSH system is organized. Plant-based foods are especially difficult because in most cases they are treated mainly as plants rather than food.

One result of treating plant-based foods as plants is that the MeSH term is usually the botanical plant name; in the case of chocolate it’s Cacao. This is usually not a serious problem when searching for specific substances because the common food name maps to the botanical MeSH term.

A more serious consequence of treating plant-based foods as plants instead of foods is that they are usually not in any food-related explosion, but only in the Plants explosion. So the only occurrence of chocolate (Cacao) is here:


The reason this is a problem is because articles on chocolate/Cacao will not be retrieved in a search for Food. So, for example, if you do a general search for food-related causes of migraine, you will not retrieve this article:

Chocolate is a migraine-provoking agent
Journal: Cephalalgia

This is not retrieved by searching for food because Cacao is not in the Food explosion. More broadly, however, it’s also not retrieved with the comprehensive Food-Diet-Nutrition hedge that we’ve discussed previously, which includes text-words as well MeSH terms and explosions.

Here are several other articles on health and medical aspects of chocolate that are not retrieved by our broad Food-Diet-Nutrition hedge:

If chocolate were the only case of a plant-based food that is not retrieved in a broad PubMed search for food-related topics, it would be a trivial matter. But that’s far from being the case. There are many plant-based foods that have the same problem in PubMed. We will be writing on several of these foods in the next few months, so keep an eye on this space!



Medical & Nursing Journals – A Twitter List

By Sarah Andrews and Eric Rumsey

Many medical and nursing journals now use Twitter. On their Twitter sites, they share links to journal articles and sometimes other news items in the field. We have made a Twitter list with 116 of these journal sites:

The base of our list is the National Library of Medicine’s list of Core Clinical journals. There are 119 titles in that list, and we were able to find Twitter feeds for about 75 of them. The other Twitter sites on our list we found in Laika Spoetnik’s Twitter journal list and from Googling likely word combinations.

Not all tweets are for journal articles. The proportion of tweets that are journal articles, as opposed to other news items, varies in different journal feeds.



Holy Carnitine! @Altmetric Is On To Something Big!

In our previous article, we talked about a ranking list done by Altmetric of the most popular research articles of 2013. An interesting anecdotal story at the Reference desk just a couple of days after publishing the article, I think, gives strong confirmation of the validity of the Altmetric ranking.

As I was working at the Reference desk, a library patron using a workstation in the reference area [who turned out to be Charles Rebouche, see more below] asked for help with a printing problem he was having. As I approached his station I couldn’t help noticing that the article he was trying to print was on Carnitine, which happened to be a prominent subject of one of the articles that was on the Altmetric ranking. I was especially struck when I noticed this because before I saw the Altmetric ranking list in December, I had never heard of carnitine. As I learned in writing about the Altmetric ranking though, it turns out that carnitine is an ingredient of red meat (and also many energy drinks) that’s implicated in new research as a possible contributor to cardiovascular disease.

After the patron’s printing problem was resolved, I talked to him about his interest in carnitine. Interestingly, I learned that he’s an emeritus faculty member who has spent much of his career on researching carnitine. I told him about my work with the Altmetric list, and about the article that was ranked as being one of the most popular research articles of 2013. He knew all about the surge in popularity of the subject that accompanied the article, he said, because he’s been asked to “come out of retirement” to do a presentation about carnitine, which is why he was in the library catching up on the latest research.

So, on one level, a cute, satisfying story about the rewards of working at the Reference desk. But beyond that, I think this little story shows that the Altmetric ranking is more than an abstract application of “big data,” that Altmetric popularity does indeed have a real effect that’s felt by real researchers!

[Dr. Rebouche has read and approved of this article. He has indeed done voluminous research on carnitine, as attested by his 41 PubMed citations!]


Food, Diet & Nutrition: Popular Subject, Difficult PubMed Search

By Eric Rumsey and Janna Lawrence

In December, Altmetric published a list of the most popular research papers of 2013 <>. The Altmetric site has developed a method to quantify popularity by using social media and traditional media to measure the “buzz” about particular articles. Of the top 64 articles on the altmetric list, a surprisingly high 19% of them (12 articles) are on food, diet and nutrition (FDN). In comparison, by our count the number of citations in the top 64 for other popular topics are: Brain/Neuro 9, Sleep 5, Heart/Cardio 3, and Cancer 3.

The popularity of FDN strikes us especially because we have recently written on this blog about the difficulty of searching FDN subjects in PubMed. The Altmetric list provides a good opportunity to test our ideas on FDN subjects that are identified by Altmetric data as being especially  popular.

Shown below are the 12 articles in the top 64 articles in the Altmetric ranking that are on FDN, with PubMed links and FDN-related MeSH terms that are used for each of the articles (the asterisk after some headings indicates that the subject is given major emphasis in the article). At the end of the list, we’ll have a few brief comments on MeSH indexing problems.

FDN-related articles on the Altmetric Top 100 Research Articles of 2013

#2 (See comments on this article at bottom)
Primary Prevention of Cardiovascular Disease with a Mediterranean Diet
New England Journal of Medicine
FDN-related MeSH terms:
Diet, Fat-Restricted
Diet, Mediterranean*
Dietary Supplements
Plant Oils*

Association of Nut Consumption with Total and Cause-Specific Mortality
New England Journal of Medicine
FDN-related MeSH terms:
Diet Surveys

#15 (See comments on this article at bottom)
Impact of insufficient sleep on total daily energy expenditure, food intake, and weight gain
Proceedings of the National Academy of Sciences
FDN-related MeSH terms:
Weight Gain/physiology*

The Autopsy of Chicken Nuggets Reads “Chicken Little”
The American Journal of Medicine
FDN-related MeSH terms:
Dietary Fats/analysis
Dietary Proteins/analysis
Fast Foods/analysis*
Poultry Products/analysis*

Myths, Presumptions, and Facts about Obesity
New England Journal of Medicine
FDN-related MeSH terms:
Breast Feeding
Diet, Reducing
Obesity*/prevention & control
Weight Loss*

Prospective Study of Breakfast Eating and Incident Coronary Heart Disease in a Cohort of Male US Health Professionals
FDN-related MeSH terms:
Food Habits*

DNA barcoding detects contamination and substitution in North American herbal products
BMC Medicine
FDN-related MeSH terms:
Not yet indexed

Persistence of Salmonella and E. coli on the surface of restaurant menus
Journal of Environmental Health
FDN-related MeSH terms:
Food Microbiology*
Foodborne Diseases/microbiology
Foodborne Diseases/prevention & control*

Meat consumption and mortality – results from the European Prospective Investigation into Cancer and Nutrition
FDN-related MeSH terms:
Diet/adverse effects*
Feeding Behavior*
Nutrition Surveys

The Relationship of Sugar to Population-Level Diabetes Prevalence: An Econometric Analysis of Repeated Cross-Sectional Data
FDN-related MeSH terms:

Inverse relationship of food and alcohol intake to sleep measures in obesity
Nutrition & Diabetes
FDN-related MeSH terms:
This journal is not currently indexed in PubMed/MEDLINE

#64 (See comments on this article at bottom)
Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
Nature Medicine
FDN-related MeSH terms:

Our comments on the Altmetric list

The twelve FDN citations in the Altmetric rankings cluster around three subjects – Plant-based foods: #2, #8, # 33; Obesity & Weight Gain: #15, #23, #58, #60; and Meat: #19, #54, #64. In a brief examination of the list, we can see that there are MeSH problems in each of these areas, most notably in these citations, one in each of the three clusters:

  • Plant-Based Foods (Not a MeSH term – For our clarification, see here)- #2 (Primary Prevention of Cardiovascular Disease with a Mediterranean Diet) – Olive oil, a major top of this article, is indexed in MeSH as Plant Oils. This is not in the Food explosion, or any other FDN explosion, so it’s not picked up by a comprehensive search for FDN subjects.
  • Obesity and Weight Gain – #15 (Impact of insufficient sleep on … food intake, and weight gain). This is indexed in MeSH as Weight gain, and not as Obesity. The latter term is retrieved by a broad FDN search because it’s in the Nutrition disorders explosion. The seemingly closely-related term Weight gain is not in that explosion, and is therefore not retrieved in a broad FDN search.
  • Meat – #64 (Intestinal microbiota metabolism of … red meat, promotes atherosclerosis) - “Red Meat” is generally considered to be beef, pork and lamb – Because none of these has separate MeSH terms, the article is indexed only as Meat. This is a problem because when that term is searched in PubMed, it is automatically exploded, and the exploded heading includes not just meat, but also fish and poultry. Even when searching for Meat as an unexploded term includes some articles for poultry and fish.

We have written previously on the problems of searching in PubMed for Plant-Based Foods. We will write in the future here on the other topics above – Obesity and Meat.


  • Thanks to Colby Vorland (‏@nutsci) who first noted in a tweet the popularity of FDN in the Altmetric ranking.
  • Thanks to Chris Shaffer, for a close reading of our article and useful comments.

AccessMedicine and AccessPharmacy Changes

Last week, McGraw-Hill released new versions of AccessMedicine and AccessPharmacy.  Because of this, some of the links to electronic books in the InfoHawk and Smart Search catalogs no longer work.  We are aware of this and are working to fix it.  In the meantime, if you are looking for a book whose link no longer works and you know you previously used it in either AccessMedicine or AccessPharmacy, you can go directly into the resource from the link under Popular Resources on Hardin’s home page.  Once you are in AccessMedicine or AccessPharmacy, click on Readings.  From the Readings page, you will see thumbnails of book covers, arranged alphabetically. Click on the cover of the book you are looking for to go into it.

At this point, we know of three  books which has been removed from AccessMedicine:

  • Current Diagnosis and Treatment in Orthopedics (Hardin owns this in print.  Call number RD 734 .C87 2006)
  • Current Diagnosis and Treatment Otolaryngology (We have ordered a print copy of this title, since electronic access is no longer feasible.)
  • Smith’s General Urology, 17th ed. (Hardin owns print of this edition and of the 18th edition, which is on Permanent Reserve.  Call number RC 871 .S5  2013)

If you have questions about these changes, please contact your liaison, or the Hardin Library Reference staff at 319-335-9151 or


ClinicalKey Now Available!

(We originally announced that ClinicalKey was available yesterday, but discovered some issues with it.  It seems to be running fine now, both on-campus and off, but if you have any problems, do not hesitate to contact us at 319-335-9151.)

Elsevier’s ClinicalKey is now available through the Health Sciences Resources A-Z list, as well as through the All Databases A-Z list.  ClinicalKey will replace MDConsult in mid-January 2014, and includes most of the content currently in that resource, plus more.  All content can be searched through a single search box, or specific types of information can be selected from the top of the screen.

Clinical Key includes:

  • Over 1100 Elsevier biomedical books*
  • More than 500 journal titles*
  • Clinical monographs from First Consult
  • Procedures Consult content and videos
  • Practice guidelines
  • Clinical Pharmacology drug monographs
  • Patient education information

Although ClinicalKey can be used without individual registration, creating an account allows users to use special features, such as accessing PDFs of most book chapters (all books have HTML chapters), saving searches, and creating presentations using ClinicalKey content.

A ClinicalKey user guide is available at  ClinicalKey is available off-campus to UI students, faculty, and staff by logging in with your HawkID and password.  Questions?  Contact your liaison or the Hardin Library reference staff at 319-335-9151 or

*Records for books and journals will be available soon in the InfoHawk catalog and the Electronic Journals list.



KNODE : new research collaboration tool available at UI

The University of Iowa has partnered with KNODE Inc. to help connect researchers at Iowa and elsewhere and to provide direct links to scientific content.

KNODE is a Cloud-based tool which provides a comprehensive view of a researcher’s expertise. Currently, KNODE is focused on researchers in the life sciences. Researcher profiles are automatically generated from a variety of data sources, including MEDLINE/PubMed journal articles, NIH grant projects, biomedicine patents, and

KNODE automatically generates and continuously updates expert profiles, eliminating the requirement for manual editing. If you wish, you call also claim your automatically generated profile to update certain information.  There are currently 3 million profiles available in KNODE.


Exam Master added a new mode – Learning

Exam Master now includes a new learning mode.  You can view the correct answer choice and question explanation immediately without generating a score report.

4 modes are available in Exam Master

1. Test Mode: Submit an answer choice for each question and click score to complete the session.  If score report access is allowed, go to My Stats to evaluate your strengths and weaknesses by topical area.

2. Review Mode: Available after an exam is scored in test mode.  Compares answer choice previously selected in test mode in correct answer choice and allows access to question explanations.

3. Study Mode: Review question feedback and access to an explanation upon submitting an answer choice for each question.  A score report is generated using the first answer choice submitted.  Click score to complete the study session.

4. New Learning Mode: View correct answer choice and question explanation immediately and learn the question content without generating a score report.

Exam Master includes material on:

Cytology and Histology
Internal and Clinical Medicine
Medical Microbiology
Clinical Modules for Physician Assistants
Medical Subject Review for Physician Assistants
PANCE/PANRE Certification Review – Updated July 2013
Dental Subject Review for NBDE Part I
Family Medicine Certification Review
General Pediatrics Certification Review
General Surgery Certification Review
Internal Medicine Certification Review
SPEX (Special Purpose EXamination)
Pharmacy Review (NAPLEX)
Supplemental Medical Sciences for Pharmacy
USMLE Step 1 Board Preparation
USMLE Step 1 Medical Subject Review
USMLE Step 2 CK Board Preparation
USMLE Step 2 CK Medical Subject Review
USMLE Step 3 Board Preparation
USMLE Step 3 Medical Subject Review


PubMed’s Secret Ingredient: Explosions

By Eric Rumsey, Janna Lawrence, and guest author Chris Shaffer, former Hardin librarian, now University Librarian, Oregon Health & Science Univ

Explosions are a powerful, built-in feature of PubMed that make it easy to search for clusters of related subjects. Because they’re so seamlessly incorporated into PubMed, it’s possible to search the database without having any knowledge of explosions. But to get the best results, it helps to understand how they work.


The clip from the MeSH database to the left gives an idea of the hierarchical “tree structure” of explosions. When you search in PubMed for a MeSH term that’s at the top of a category, the search automatically includes all of the terms indented under it. So for instance, if you search in PubMed for Cardiovascular Abnormalities, the two terms indented under it are also included. The “+” sign after these terms indicate that they are explosions that have other terms under them, which are also included.

To see details of specific exploded terms, search the MeSH Database. (To see the page for Cardiovascular Diseases, in the example at left, click the graphic, or click here)

Much of the elegance of explosions is the ability to search large categories, and to move up and down “the tree” to try out more or less specific terms. For example, let’s say you’re interested in the subject of exercise and heart diseases. Combining those concepts in PubMed, you find there are more than 7000 citations. So, how many citations are there about the broader concept of cardiovascular diseases and exercise? With the power of PubMed’s automatic explosions, it’s easy to see that there are about double the number. And, of course, it’s easy to move the other direction in the tree, to do the search with specific terms and explosions anywhere in the hierarchy.

Another key reason explosions are so valuable is that articles are indexed only to the most specific MeSH term. An article on Cardiac Tamponade, for example, will only be assigned that term, and not the broader term Heart Diseases. Without explosions, it would not be found by searching for Heart Diseases. But because it’s in the Heart Diseases explosion, it is found.

Why “Secret Ingredient”?

We call explosions PubMed’s “Secret Ingredient” because they are very powerful but little-known and/or taken for granted. It wasn’t always this way – When the Medline database (which is what you’re searching in PubMed) was in its early days, in the 1980′s, explosions certainly were acknowledged to be a “big deal” – With the relatively low-powered computers of the time, explosions took big chunks of computer time, and were used with caution. With today’s computers, of course, this is only a distant memory, and, fortunately, no one needs to worry about using explosions.

A further reason that explosions have receded into the background is that, with the advent of Google-style simple search interfaces, PubMed has adopted the same sort of simple interface. This has had the effect of making people less aware of what PubMed is doing “under the hood.” With the simple, Google-like interface of PubMed, it’s natural to think that it works “just like Google.” But in fact it’s quite different - With only a bit of oversimplifying, the basic difference is that Google searching is purely computer-based and PubMed is based on human indexing. Humans actually read every article in PubMed, and assign 10-15 MeSH terms, which is what makes explosions possible.

How to search without an explosion

When you search for a subject in PubMed, the default is for it to explode the MeSH term that’s associated with the subject, and this is almost always what you want, since articles are indexed with the most specific term available. For example, an article about cardiac arrhythmias will be indexed as Arrythmias, Cardiac, and not to its broader heading, Heart Diseases. There may be occasions, however, when you only want the MeSH term at the top of the category, without subsidiary terms. The way to do that search, using the example discussed here, is to search for: Heart Diseases [mh:noexp]. Another way to do this is to click the box that says “Do not include MeSH terms found below this term in the MeSH hierarchy” on the MeSH Database display for Heart Diseases.

0 now available online from Hardin Library

AnatomyTV Launch PageHardin Library for the Health Sciences is excited to announce that is now available for our patrons! is an internet-based anatomy tool provided by Stat!Ref which includes a complete set of 3D human models. allows for manipulation and 360-degree rotation of virtual models, as well as filtering different layers of anatomical structure. Additionally, links to relevant text, clinical images, diagrams, scans, and videos. Supplementary information such as quizzes, MCQs, and patient information are all available for download.

To begin using, simply go to the Hardin Library website and select the tool from the Health Sciences Resources A-Z list.  Direct access is also available at

Please note that access to is limited to a set number of users, so if you encounter problems using this resource please feel free to contact Hardin Reference staff at 319-335-9151 or and we will provide assistance.