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Aug 11 2016

US Lags Behind The World In Plant-Based Food Research

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Many other countries spend a much larger proportion of their research time and resources on plant-based foods than the United States does.

By Xiaomei Gu, Eric Rumsey and Janna Lawrence

In our explorations of plant-base foods (PBFs) in PubMed, it’s often striking that there are many excellent articles from non-US countries. So we did a survey in PubMed to measure different countries’ authorship of articles on PBFs, and we found that, indeed, several countries have a much higher proportion of their total articles on PBFs than the US.

The chart above shows our data for all PBFs and the charts below show four specific foods or food groups. The charts are based on the percentage of articles from each county, not the total number of articles. So even though the total number of articles on PBFs by US authors may be higher than other countries, the proportion of articles on PBFs is substantially lower. [The charts are from a poster presented at MLA in 2016. For more details on our survey methods, see the poster. The PubMed search strategy used to find plant-based foods in the chart above is described here.]

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Jun 17 2016

Nuts as a Healthy Food: How to Search in PubMed

By Eric Rumsey, Janna Lawrence and Xiaomei Gu

This article is based on a poster presented at the Medical Library Association annual meeting, Toronto, May 2016.

Introduction

Searching for nuts as food is difficult. As with most plant-based foods, MeSH terms for specific types of nuts are in the Plants explosion instead of in the food explosion. Nuts are especially tricky because the MeSH term Nuts is not an explosion, and most articles on specific types of nuts are not indexed to the term Nuts. So it’s necessary to search for specific nuts to retrieve articles on them.

A caveat—As with nutrition topics in general, and plant-based foods in particular, searching in PubMed is complicated, largely because many plant-based substances are used as foods and also as medicines or experimental organisms. A list of articles on specific nut types is likely to contain some articles that are not food-related.

Searching for Nut Types

The general idea of searching for specific types of nuts is simple: Do an OR search that includes the common name and botanical name. In most cases, articles on a specific nut type will be indexed under the botanical name, but using the common name is always a good idea. See the example below for searching walnuts.

walnut [tiab] OR walnuts [tiab] OR juglans [MeSH]

It is necessary to restrict the search for the common names to the title and abstract [tiab] fields because there are many streets in the Address field that are named after nuts (e.g., 975 Walnut St.).

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Image 1. Almonds

 

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Image 2. Walnuts

 

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Image 3. Hazelnuts

 

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Image 4. Cashews

 

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Image 5. Pecans

 

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Image 6. Brazil Nuts

 

Peanuts Are Different!

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Image 7. Peanuts

Peanuts are a special case. Unlike the other nuts here, they grow on herbaceous plants instead of on trees and, as members of the bean family, they are nutritionally more closely related to beans than to other nuts. There is also a separate MeSH term, Peanut Hypersensitivity, dealing with peanut allergies.

Because peanuts are commonly used as experimental plants, many of the articles about them are not related to nutrition. To  focus on nutritional aspects, we suggest incorporating the Diet, Food, and Nutrition explosion into the search:

(peanut [tiab] OR peanuts [tiab] OR arachis [mh])

AND Diet, Food, and Nutrition [mh]

Citations: 2932

May 12 2016

Great but Hidden: PubMed’s New Diet, Food, and Nutrition Explosion

By Eric Rumsey, Janna Lawrence and Xiaomei Gu

As we have written, NLM made a great improvement in introducing the new explosion for Diet, Food, and Nutrition. Before that was introduced this year, each of the three elements in the explosion had to be searched separately because they were not in the same explosion. So we strongly endorse the new explosion!

Although it is less difficult to search for nutrition articles now, there is still a problem. The term mapping feature of PubMed does not work for the word “nutrition,” which is certainly a common way to search for the broad subject comprised by the new explosion.

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Image 1. Search Details for Heart Attack.

In most cases in PubMed, if the user searches a word or term that’s synonymous with the appropriate MeSH term, the system will automatically include the MeSH term in the search. An example of this is searching for the term heart attack (without quotes).

As shown in Image 1, PubMed automatically maps the word to the appropriate MeSH term – “myocardial infarction” [MeSH Terms]. (To see Search details, on the PubMed search results screen, scroll down to the “Search details” box, in the right side-bar). Another example of PubMed’s automatic mapping is cancer, which maps to neoplasms [MeSH Terms].

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Image 2. Search Details for Nutrition.

A search for the word nutrition retrieves several phrases and MeSH terms, seen in the Search details in Image 2. But this does not include the new explosion Diet, Food, and Nutrition, which would retrieve many more relevant articles than these terms do.

There are two conceivable ways that NLM could address this problem. The first is to change the name of the explosion to Nutrition, so that mapping the word would not be necessary. The second solution is to make the word nutrition map to the new explosion. We encourage NLM to consider these options, so that the full power of the new explosion can be released!

Mar 18 2016

Plant-Based Foods – An Inclusive PubMed Search – Revised 2016

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By Eric Rumsey, Janna Lawrence and Xiaomei Gu

Searching for nutrition topics in PubMed is tricky. It’s especially difficult to search for plant-based foods (PBF’s). In 2014, we published an article that addresses this problem that contained a hedge for searching for PBF’s. A few months ago, the National Library of Medicine introduced a new explosion that makes it a lot easier to search for nutrition topics in PubMed, which we discussed here.

In this article we are revising our 2014 PBF hedge to incorporate the new PubMed explosion. While there may still be a few occasions when our previous hedge for PBF’s would be appropriate, in almost all cases we do not recommend using the old hedge. Instead, we recommend using the hedge below:

((Plants[mesh] OR Plant Preparations[mesh]) AND Diet, Food, and Nutrition [mesh]) OR (Vegetables[mesh] OR Fruit[mesh] OR Plants, Edible [mesh] OR Dietary Fiber[mesh] OR Flour[mesh] OR Bread[mesh] OR Diet, Vegetarian[mesh] OR Nuts[mesh] OR Condiments[mesh] OR Vegetable Proteins[mesh] OR Tea[mesh] OR Coffee[mesh] OR Wine[mesh] OR Vegetable Products[mesh])

The big change in this PBF hedge from the previous PBF hedge is, of course, replacing the food-diet-nutrition hedge that was part of the previous PBF hedge with the the new Diet, Food, and Nutrition explosion. Otherwise, the main change is the addition of the new MeSH term Vegetable Products.

Advanced techniques for plant-based food searching

In most cases, you’ll probably want to start with the hedge above. But if that doesn’t find what you want, try the ideas below.

If you combine your subject (a particular disease for example) with the hedge above and it misses articles that you think exist, consider broadening the search by combining your subject with Plants. The Plants explosion in MeSH is very large, containing hundreds of plant species. It’s organized by taxonomic relationships, which makes it hard for a non-botanist to browse. But it’s useful to combine with other subjects in searching, because it’s so comprehensive. The main drawback in searching it is that in addition to plant-based foods, it also has many plant-based drugs, which you’ll have to sift out from the food articles.

If you combine your subject with the hedge above and it misses articles on particular plant-based foods, search specifically for those. If you do a search for food and migraine, for example, and your search doesn’t pick up specific foods that you know have been associated with migraine (e.g. chocolate), combine those foods specifically with migraine.

A caveat: There is an exploded MeSH term Plants, Edible, which might seem to be a good place to search for plant-based foods. Unfortunately, however, it’s of limited usefulness – The explosion contains only grain plants and Vegetables, which is mainly soy-based foods. The term Plants, Edible itself is mostly used to index articles that are on the general concept rather than articles on specific types of edible plants.

If you’re interested in reading some background explaining why it’s so difficult to search for PBFs in PubMed, see our companion article.

Mar 18 2016

Diet, Food, and Nutrition – How To Search in PubMed

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By Eric Rumsey, Janna Lawrence and Xiaomei Gu

Searching for Food, Diet & Nutrition has long been one of the most difficult subjects to search in PubMed. We were happy to report earlier this year that the National Library of Medicine has gone a long way toward fixing this problem, with a new explosion for Diet, Food, and Nutrition.

Before the new explosion came out, searching for the subject was very tricky because diet, food and nutrition were all in different places in the MeSH tree structure, and so they had to be searched separately. To help with this problem, we created a detailed search strategy, or hedge, that would bring together all of the components in one search. We no longer recommend using this hedge. We have examined the new explosion, and find that it covers the field very adequately.

We strongly recommend the new explosion for most nutrition searches. But there are some aspects of the field that are not covered in the new explosion that were part of our hedge, in particular obesity and vitamins. Both of these terms are closely connected to the subject of food, diet & nutrition. But we understand why NLM has not included them in the new explosion, since they will not always be wanted. Both of these subjects are somewhat complicated to search in PubMed. In both cases, however, a simple one-word text word search will retrieve almost all of the relevant citations. So in cases when you want to include these subjects in your nutrition searching, you can do these searches:

Diet, Food, and Nutrition [mh] OR vitamins
Diet, Food, and Nutrition [mh] OR obesity
Diet, Food, and Nutrition [mh] OR vitamins OR obesity

“Good job, NLM!”

In conclusion, good words for the National Library of Medicine – Thank you for fixing the long-standing problem in searching for nutrition! With the surging interest in the subject, you’ve made things a lot easier for the many people searching for it.

Feb 24 2016

New Resource: The Medical Letter (site license) and its Mobile App

Hardin Library for the Health Sciences now has a site license for the Medical Letter at http://purl.lib.uiowa.edu/MedLetter.  Medical Letter can also be found on the Health Sciences Resources A-Z http://guides.lib.uiowa.edu/az.php .

The Medical Letter’s home page shows the current issue of The Medical Letter on Drugs and Therapeutics.

  • To view full text articles and to find the  Download PDF link, click on the title of the article.
  • Use the navigation links on the left side of the screen to access other contents, including previous issues, continue education (CME/CE), Drugs for Parasitic Infections, and The Handbook of Antimicrobial Therapy.

Note that the library also has print copies of the Medical Letter on Drugs and Therapeutics, Drugs for Parasitic Infections, and Handbook of Antimicrobial Therapy. Search InfoHawk Catalog  for more information.

medical letter homepage

The library’s site license also allows access to the Medial Letter mobile app.

  1. Go to http://purl.lib.uiowa.edu/MedLettermedical letter app
  2. Click the Mobile Apps link under Products on the left side of the screen.
  3. Fill in the registration form using your Iowa email to set up a password.
  4. Open the App/Play Store on your mobile device, search for “the Medical Letter” and install at no charge.
  5. Log in with the password you created earlier.

Questions? Comments? Email us at lib-hardin@uiowa.edu or call (319) 335-9151.

Feb 23 2016

ClinicalKey available for iOS and Android mobile devices

screen shot clinicalkey mobile ClinicalKey provides access to more than 1100 medical texts published by Elsevier, articles from more than 500 journals, practice guidelines, drug information, and patient education handouts. Users must log in to (free for UI affiliates) personal accounts to download PDFs.

1. Open the App Store on your mobile device.
2. Search for “ClinicalKey” and install at no charge.
3. Once in the app, two options will appear – Click on ClinicalKey.
4. Enter your username and password used for accessing PDFs.
If you do not have a username and password yet, follow steps 5-7.
5. Go to http://purl.lib.uiowa.edu/clinicalkey
6. Click on the Register link at the top right of the screen.
7. Create a personal account using your Iowa email.
Feb 4 2016

EndNote X7 for MAC now works with Microsoft Word 2016

endnote_logoGood news!  EndNote X7 for the Mac now works with Microsoft Word 2016.  When you open the desktop version of EndNote, it should tell you that that there is an update available, but you can also select Check for Updates in the EndNote X7 dropdown menu.  EndNote Basic (the online only version) will also prompt you to install the new Cite While You Write plug-in for Word.  Whether you are using the desktop or online version, you also need to have the latest version of Word 2016  (currently version 15.18) installed.

Once Word and EndNote are both updated, the EndNote Cite While You Write tools should appear as a tab in Word. The first time you launch Word 2016 after updating EndNote, you will be asked to “grant access” to an EndNote .plist file. Simply click Grant Access; you should not be asked this again.

More information about the update, including some troubleshooting in case the tools do not automatically appear in Word, can be found at http://endnote.com/kb/138936.  More information about updating Word, with a more complete explanation about “granting access,” is at http://endnote.com/kb/138936.

If you have questions about EndNote, please contact your Library Liaison or Janna Lawrence.