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Plant-Based Foods – A Tricky PubMed Search

By Eric Rumsey and Janna Lawrence

As discussed in an earlier article, searching for Food-Diet-Nutrition in PubMed is difficult because the subject is spread around in several different places in the MeSH classification system. In another article, we provide a way around this, which provides a broad set of search terms that can be used to search for the subject. An aspect of the subject, however, that cannot be put in a “package” that makes it possible to search together as a group is plant-based foods.

The Food cluster-explosion contains many specific foods, as MeSH headings, including some plant-based foods. A large proportion of all plant-based foods, however, are not in the Food cluster-explosion, but are only in Plants, and not in Food. These, of course, will not be retrieved by searching for “Food.” Adding to the confusion, some vegetables (but no fruits) are in both categories. Here are some examples:

Sweet potato is put under the MeSH term Ipomoea batatas. Its only place in the MeSH tree is in the Plants explosion:

Plants
   Angiosperms
      Convulvulaceae
         Ipomoea
            Ipomoea batatas

As noted above, this will not be retrieved by searching for “food.”

Kale (MeSH term Brassica), on the other hand, is included in both Plants and Food and so it will be retrieved by searching for “food”:

Plants
   Angiosperms
      Brassicaceae
         Brassica
Food
   Vegetables
      Brassica

The examples for sweet potato and kale bring to light another point of confusion, which is that terms in the Plants explosion are usually botanical names that are not recognizable to most people. A few examples (all of which are only in the Plants explosion but not in the Food explosion):

Grapes is Vitis
Strawberry is Fragaria
Okra is Abelmoschus
Kidney Beans is Phaseolus
Chocolate is Cacao
Turmeric is Curcuma

This is usually not a problem when searching for specific food plants, because when searching for a common name, it’s mapped to the botanical MeSH term (e.g. if you search for Grapes, it maps to Vitis). The problem comes if you want to browse the Plants cluster to pick out the edible plants from the many plants that are not edible, because only the botanical names are listed. The Rose family (Rosaceae) of plants, for example, has several edible species within it. There are 19 genera listed in MeSH in the family, and 6 of them have edible species. But to find them, you have to be able to pick out the genera with edible species (e.g. Malus, Prunus) from the others (e.g. Agrimonia, Alchemilla).

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 a relatively small number of vegetables, and 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.

A qualification: What we say here about the difficulty of doing comprehensive PubMed searches that include all specific plant-based foods applies to a lesser degree to other types of foods also. Looking, for example, at Meat in the MeSH classification of Food, there are no headings for specific types of meat (e.g. beef, pork), so they’re all indexed under the broader term Meat. The reason the problem is so much more complicated for plant-based foods is because there are so many of them, and also because the line between plant-based foods and plant-based medicines is often fuzzy.

Advice on searching for plant-based foods

Consider combining Plants with your subject – 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 want to restrict your search to plant-based foods, instead of foods in general, you can combine the Plants explosion AND the Food-Diet-Nutrition hedge search discussed in a previous article.

If you combine your subject with the hedge in the previous article 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.

 

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Keep up with your favorite journals using BrowZine!

The UI Libraries now subscribes to BrowZine, an app that makes it easier to read your favorite journals on your iPad or Android tablet.  Because BrowZine knows which journals the UI Libraries subscribe to, it’s easy to find your favorite journals by title or subject and even to create a personal bookshelf of your favorite journals.  Individual articles can also be saved for reading later. Articles found in BrowZine can also be synced with Zotero, Dropbox, or other services.

Download BrowZine onto your device from the Apple App Store, Google Play, or the Amazon store.  Launch BrowZine, and select University of Iowa from the dropdown list.  You will then be asked to log in with your HawkID and password.  (You should only have to do this once.)  From there, BrowZine will know what journals the library has.  Almost all of the library’s online journals are available; if you find one that is not, please contact us.

You can watch a 2-minute video about BrowZine at http://vimeo.com/52663192.  If you have questions, please feel free to contact Hardin Reference staff at 319-335-9151 or lib-hardin@uiowa.edu.

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Food, Diet & Nutrition – An Inclusive PubMed Search

By Eric Rumsey and Janna Lawrence

As discussed in a previous article, searching for Food, Diet, and Nutrition in PubMed is tricky because the relevant Medical Subject Headings (MeSH) for the subject are scattered widely in the classification scheme. To do a thorough search, therefore, it’s necessary to use a number of terms. To make this easier, we have created a search strategy, or hedge, that combines most of the Food-Diet-Nutrition terms in one search.

The hedge search, of course, is much too large to be useful by itself (it gets over 1.5 million citations in PubMed). So it’s intended to be combined with another subject. A typical example would be finding the nutritional aspects of a disease.

Here is the hedge:

food OR foods OR beverages OR diet OR dietary OR vitamin OR vitamins OR nutrition OR nutritional OR nutrition disorders OR food industry OR nutritional physiological phenomena OR dietary fats OR dietary proteins OR feeding behavior

To use this search, click this link. You can also copy the text above and paste it into the PubMed search box. If you have a personal “My NCBI” account in PubMed, the hedge search can be saved for later use, or it can be made into a search filter. For information on setting up and using saved searches, see here; for more information on filters, see here.

List of terms in the hedge. Terms on the list that have no accompanying text are searched only as text-words (words appearing in article titles or abstracts), and as words that are part of MeSH terms.Terms below that are found in MeSH (which are also automatically searched as text-words) have brief commentary.

Disclaimer: This hedge is not ALL-inclusive for Food-Diet-Nutrition. As complicated as the subject is, it’s not possible to include all of the relevant terms in one search. This is especially the case because most plant-based foods are not in any category that can be searched together. The Food explosion does include many specific foods, but most plant-based foods are only in the Plants explosion, and not in the Food explosion. For tips on searching for plant-based foods, see here.

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Interesting Articles on Altmetrics

In a previous post, we mentioned the concept of altmetrics briefly when introducing the Altmetric for Scopus feature in the Scopus database.  Below we are listing links to two thought-provoking articles on altmetrics, both published last week.

The following two blog posts published in 2012 are also interesting. Make sure to check out the comments, which are equally interesting.

Hardin Library offers workshops on a variety of subjects including how to find journals’ Impact Factors and H indices. Our Fall schedule is coming soon. Stay tuned.

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UpToDate Mobile App now available!

UpToDateMobileUpToDate is one of the leading evidence-based clinical practice tools available, and has long been provided for University of Iowa students, faculty, and clinicians. Written by a recognized faculty of experts who each address a specific clinical issue, the contents synthesize the latest evidence and best practices.

Now, access to this resource has become even more convenient for mobile device users with the introduction of the UpToDate mobile app.

In order to access this resource, members of the University of Iowa Community can simply register for an account at http://www.uptodate.com using a valid @uiowa.edu email address. Users will receive a confirmation email, after which the app can be downloaded and initiated with full entrée into thousands of topic areas. Note that full-text of linked content isn’t directly available from within the app interface.

The app is available for iOS, Android, and Windows 8.

Please contact Hardin Library with any questions of comments!

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Searching for Food, Diet & Nutrition in PubMed

By Eric Rumsey and Janna Lawrence

Much of the power of PubMed searching is due to the elegant Medical Subject Heading [MeSH] system used to index articles. When you type words into the PubMed search box, it looks for the most appropriate MeSH terms to use for your topic. When PubMed searches those MeSH terms, it also searches for closely related terms that are narrower in scope. This is especially useful because it makes it easy to search for broad categories of subjects. Search for cancer, for instance, and you’ll get every type of cancer, from leukemia to melanoma, whether the actual word cancer is used or not. The MeSH system works well for most all subjects in PubMed. A glaring exception, however, is food and nutrition.

Unlike most other subjects, to do a comprehensive food and nutrition search, it’s necessary to search for at least four different concepts:

  • Food and Beverages (a MeSH term)
  • Nutritional Physiological Phenomena (a MeSH term, which includes Diet as a narrower term)
  • Diet Therapy (a subheading)
  • Nutrition (Unlike the concepts above, this is actually not a MeSH term; it includes searching for the word nutrition as a text word, and several MeSH terms that use the word nutrition or nutritional)

Unfortunately, the articles that are indexed with terms in these clusters often do not overlap. Many articles are in only one of the clusters. Making things even more complicated, there are some aspects of the subject that are not included in any of these broad concepts. This is especially the case when searching for specific food ingredients or nutritional supplements. Here are a some examples that illustrate this — these articles are not indexed with any of the general nutritional MeSH terms mentioned above:

New post: How to do a comprehensive food and nutrition search by creating a saved search or search filter in PubMed.

UI affiliates: For help with food and nutrition searching in PubMed, please contact librarians at Hardin.

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DSM-5 Now Available Online

The DSM-5 is now available online through the American Psychiatry Association’s Psychiatry Online platform.  It is available at http://purl.lib.uiowa.edu/dsm.  The link can also be found by searching DSM-5 in Smart Search or InfoHawk.

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Systematic Reviews and Meta-Analyses

Systematic reviews and meta-analyses have long been considered one of the highest levels of evidence, and lately, publication frequency in health science journals is on the rise.  However, there are still a lot of people who are unaware of what goes into writing a systematic review or a meta-analysis. This post will discuss what a systematic review entails, how it differs from a meta-analysis, and the value that librarians bring to both types of studies.

A systematic review is a research study that seeks to find all the high quality studies done on a given topic so that they can be summarized into one article.  If the studies are homogenous or similar enough to one another, the data can be extracted and combined using statistical formulas. This statistical compilation of data is a meta-analysis. Not all systematic reviews contain a meta-analysis, but all citations to be included in a meta-analysis should be located through a systematic search, to reduce the risk of bias.

An important part of preparing a systematic review is to ensure that the method used is explicit and transparent, allowing for another team to replicate the process. The first step involves putting together a team of at least two researchers who will independently review the studies located.  These researchers then develop a research question and write up a protocol that explicitly detailing how the systematic review will be carried out. One of the details is the criteria against which studies will be assessed for inclusion in the review. It is highly recommended that researchers register their protocols before they begin the formal search for studies.  Once the protocol is in place, the search for and review of high quality studies can begin. Systematic reviews can take anywhere from one year to eighteen months to complete due to the rigorous nature of the review process. Librarians are highly skilled and trained to develop what are often complicated and lengthy search strategies in order to locate as many relevant studies as possible.  They are also familiar with standards and basic steps for completing a systematic review. In the report, Finding What Works in Health Care: Standards for Systematic Reviews, the Institute of Medicine recommends working with a librarian or other information specialist to plan out the search strategy and to peer review the final strategy used to locate studies. Three of the librarians are Hardin Library have attended the Systematic Review Workshop: The Nuts and Bolts for Librarians which takes place over the course of two and a half days.

If you would like to learn more about conducting and locating systematic reviews, please see the Systematic Review LibGuide. You are also welcome to contact us if you have any questions.

Image of Getting Help page on guide

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Print DSM-5 Available at Hardin Library

A print copy of the DSM-5 is now available in the Hardin Permanent Reserve collection, under call number RC 455.2 .C4 D54 2013.  It may be checked out for two hours at a time.

We have had several questions about whether we will be adding the electronic version of the DSM-5.  The quick answer is yes, we will!  The longer answer is that we have to wait for it to actually be available.  We get the electronic version of the DSM through the American Psychiatric Association’s Psychiatry Online platform.  They have informed us that the DSM-5 will be added sometime this summer.

If you have questions about how we acquire new resources, please contact Janna Lawrence at janna-lawrence@uiowa.edu or 319-335-9870.

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Measuring Scholarly Impact: Altmetrics and Altmetric for Scopus

Traditional scholarly metrics like Journal Impact Factors do not take into account scholars’ impact in today’s social media world.  This is where altmetrics come in (visit altmetrics: a manifesto for more information). There are a growing number of altmetrics applications out there. One example is the Altmetric for Scopus.

Scopus is a multidisciplinary database with substantial international coverage. When you view an abstract in Scopus, you might see a box titled Altmetric for Scopus on the right side of the screen.  Below is a screenshot taken from the abstract view of the article: Slinin, Y., Paudel, M., Taylor, B. C., Ishani, A., Rossom, R., Yaffe, K., . . . Ensrud, K. E. (2012). Association between serum 25(OH) vitamin D and the risk of cognitive decline in older women. Journals of Gerontology – Series A Biological Sciences and Medical Sciences, 67 A(10), 1092-1098.

It should be noted that Scopus is not compatible with Internet Explorer (IE) 9 (like ProQuest Dissertations and Theses). IE 9 users should also make sure compatibility view mode is turned on: go to Tools and then click on Compatibility View settings and check Display all websites in Compatibility View.

altmetric for scopus

Altmetric for Scopus is a 3rd party web application that collects mentions on social media and news outlets and counts on popular reference managers for a  particular paper.  The number inside the colored circle is the Altmetric score for the article you’re viewing.  If you don’t see the Altmetric for Scopus, it means this app can’t find any mentions of the article you are viewing in their data sources. Also keep in mind that Altmetric only started collecting content from supported publishers/repositories during the second half of 2011.  Read more on the app’s potential limits on its developer’s website.

Come to Hardin Library on Tuesday, Feb 19th, 1:00-2:00 pm and learn more about Scopus. Register for the class at http://www.lib.uiowa.edu/hardin/workshop/ Don’t forget that we offer a class called “Get Started Publishing”. If you don’t see it listed, you can always contact us for a one on one or group consultation.