Plant-Based Foods – A Tricky PubMed Search

This article has been superseded by the following:
Plant-Based Foods – A Tricky PubMed Search – Revised 2016

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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

[9.4.14. For comprehensive searches on plant-based foods, see the hedge in our newly published article]

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.


The Plant-Based Foods category has links to additional articles we’ve written on searching plant-based foods in PubMed.

Food, Diet & Nutrition – An Inclusive PubMed Search

[March, 2016 – With NLM’s recent introduction of an inclusive diet, food and nutrition explosion, in most cases we recommend using the new explosion instead of the hedge described below. Please see our article on the new explosion.]

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 (below). 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.

Searching for Food, Diet & Nutrition in PubMed

This article has been superseded by the following:
Diet, Food, and Nutrition – How To Search in PubMed

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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:


Here are additional articles we’ve written on searching food, diet and nutrition in PubMed:

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

PubMed Limits Are Now Filters

As you may have noticed, PubMed changed the way users limit search results. The link for “limits” has been replaced by a “filters” sidebar. This sidebar will function similarly to the way the limits page worked. For example, once filters/limits have been set, they will remain in place for all subsequent searches unless the user turns them off.

One difference users might notice is that filters will not show if they are unavailable or not applicable for a search. For example, if you run a search on a topic where there hasn’t been a meta-analysis done, the option to limit your search to meta-analyses will not be available.

A feature that should be used with caution is the “Text Availability” filter located prominently at the top of the filters bar. Remember that these filters are for people that do not have access to a health sciences library. Students, faculty, staff, residents and fellows of the University of Iowa should avoid these filters and use our InfoLink button instead (which is seen when you access the abstract view). This will ensure that high quality articles are not missed. Remember that University of Iowa affiliates can also take advantage of our free interlibrary loan service. http://www.lib.uiowa.edu/hardin/illa.html

To learn more, please check out this tutorial on NLM’s YouTube channel http://www.youtube.com/watch?v=KGs547njZ7U&feature=youtu.be, read NLM Technical Bulletin http://www.nlm.nih.gov/pubs/techbull/mj12/mj12_pm_sidebar.html or feel free to contact Hardin Librarians a http://www.lib.uiowa.edu/hardin/contact.html

Changes to PubMed

There are a few new features available in PubMed this week. There is now an option within a single citation abstract view to add items to favorites. This is similar to the clipboard function, but requires that you are signed in to your NCBI account (which is free and allows you to save searches, create folders and share citations.) This allows you to easily save citations permanently to your collections.

The other recent change is the addition of a menu option to send citations to a citation manager. This works very well for importing citations into Endnote.

Here is a series of screen captures to demonstrate the process for Endnote Import  using Microsoft’s IE 9.

Step 1: Select desired citation and then use the send to menu on the top right side, select citation manager radio button, and then select create file.

Step 2: If you are using IE, select open when prompted.

Step 3: Choose PubMed import filter and references will be imported.

Other browsers may perform differently. For example, in Firefox, steps 1 and 2 are the same but the file open prompt is different.

For Refworks Import,  instead of opening file, save file instead.

Follow steps 1 and 2 but then save file generated instead of opening (both IE and firefox).

Select the appropriate import filter, attach saved file, and import.

If you have any questions about these features or about how to use any of these tools, please contact your liaison librarian. http://www.lib.uiowa.edu/hardin/liaisons.htm

Or watch these PubMed tutorials for help: http://www.nlm.nih.gov/bsd/disted/pubmed.html#qtex .

PubMed and Internet Explorer 6

As of September 1, PubMed may no longer work with IE 6. The current version of Internet Explorer is IE 9 and if you look at the Microsoft Internet Explorer download page, it doesn’t go back further than IE 7.

You can find out which version of Internet Explorer you are using, you can find that information listed at the top of the browser under “Help” and then “About Internet Explorer” or under the gear icon on the top right of the browser and there is an option for “About Internet Explorer” near the bottom of the list.

If you are located within the hospital, you might want to contact HCIS to see if they can update your browser.  Other users should contact their IT support folks if they do not have administrative rights to their computers.

Another option is to work through Virtual Desktop. This site allows UI users to utilize software programs without downloading them to a computer.

If you have any questions or comments about accessing or using PubMed, feel free to contact us at (319) 335-9151 or lib-hardin@uiowa.edu.

 

Changes Coming to My NCBI

My NCBI is going to be getting a little bit of a make-over in the near future. If you are not familiar with My NCBI, it is most known for being a tool that allows you to save searches, set auto-alerts in PubMed, and manages your “My Bibliography” (which is used for managing your personal publications and NIH grant funding).  There are quite a few changes coming, but we’ll just focus on the ones that are most noticeable.

My NCBI Homepage

At this time, it’s not always easy to see what is available in My NCBI, but coming soon, the main page will be streamlined so that most features can be accessed from the main page. From the preview, it appears that the options will be laid out in titled boxes such as: My Bibliography, Filters, Saved Searches, etc.

Image of the new My NCBI landing page

Saved Searches

With the new Saved Searches box, you can set up an auto-alert if you want to receive an email when new research is published, or you can create a permanent saved search.  Within MyNCBI, there will be a table set up to show you when you last ran a search, how many new citations have become available since then, and a link that lets you go directly to the new stuff.

Image of My NCBI Saved Search Screen

My Bibliography

This is the area of My NCBI can be used to create a list of the articles that you have personally published. This list can be private or shared with others, and now, you can designate someone other than yourself to add and make changes to this part of your account without giving them your personal login information.  You also have more options for how you would like to display and share these citations. One display option lets you link your account with the eRA commons and see whether or not your articles are in compliance with the NIH Public Access Policy.

Image of My Bibliography when linked to ERA

 If you would like to know more about these changes and the many others that are coming to My NCBI, check out the NLM Technical Bulletin: My NCBI Redesign.

As always, if you have any questions about using My NCBI, PubMed or other library resources, contact us. We’re happy to help.

MeSH database redesign launched February 14

Have you noticed that PubMed looks a little different when you’re using MeSH?

The National Center for Biotechnology Information (NCBI) Medical Subject Headings (MeSH) Database was redesigned on February 14, 2011 to provide users with the same streamlined interface now available in PubMed® and the NLM® Catalog. If you haven’t heard of MeSH, it stands for medical subject headings and is a wonderful way to find relevant articles when searching.

What does this mean for you? Well, it means a much cleaner design within the MeSH database.  One of the best features is that the subheadings are now arranged into neat columns rather than in one jumbled paragraph. Another lovely feature is the PubMed Search builder that now shows up on the right side of the page.

Screenshot demonstrating columns for MeSH subheadings

If you’d like to learn more about all the changes that have taken place, you can check out the NLM Technial Bulletin that was updated on February 14 of this year.

New Doors to PubMed

As the volume of content in PubMed continues to expand, the need for sophisticated and skillful searching is more important than ever. In addition to developing fluency with MeSH and limits, however, today’s researchers have access to an increasing number of third-party, home-grown, and open-source tools with which to refine their literature searches.

One such resource is the intriguing PubReMiner (http://bioinfo.amc.uva.nl/human-genetics/pubreminer/), which is a front end search overlay that allows PubMed searchers to view search results in frequency tables. This provides an interesting lens for focusing subsequent queries and optimizing results. PubReMiner is web-based, operating system agnostic, and free-of-charge.

For example, a search for terms such as BRAIN NEOPLASM “STEM CELL” TREATMENT might result in a set of frequency tables which would reveal the frequency of each (and all) of the terms as they occur in a variety of fields, such as Journal Title, Country of Origin, or Author.

Using these tables, PubReMiner then allows a user to select terms by checking boxes  to create a query string that can be sent directly to PubMed!

This is only one example of the emerging breed of search tools that are available for your experimentation and use. If you’d like to learn more, please contact Shane Wallace, the Emerging Technologies Librarian at Hardin!