Is Chocolate A Food? A Problem In PubMed – 2016 Update


By Eric Rumsey, Janna Lawrence and Xiaomei Gu

As we’ve written, searching for plant-based foods (PBFs) in PubMed is difficult because of the way the MeSH system is organized. This is especially the case because because in most cases PBFs are treated 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 by the Diet, Food, and Nutrition explosion.

Here are several other articles on health and medical aspects of chocolate that are not retrieved by the broad Diet, Food, and Nutrition explosion:

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 have written about a few of these.

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Plant-Based Foods – A Tricky PubMed Search – Revised 2016


By Eric Rumsey, Janna Lawrence and Xiaomei Gu

As we discussed in an article earlier this year, searching for nutrition in PubMed has improved greatly since NLM brought the subject together in one explosion (Diet, Food, and Nutrition). This ability to search the field of nutrition easily has helped in searching for plant-based foods [PBFs] in some ways. But in other ways, it’s still as difficult as it was when we wrote our 2013 article on the same topic.

The basic problem in searching for PBFs, just as it was before the addition of the new explosion, is that a large proportion of PBFs are not in the Food explosion, but are only in Plants, and not in Food. So the fact that Food is part of the new inclusive explosion doesn’t make it any easier to search for PBFs.

In addition to the fact that most fruits and vegetables are treated as plants instead of foods, another problem in searching for them is that almost all of them are put under their botanical, Latin names, that are not recognizable to most people. Here are some examples, all of which are in the plant-taxonomic branch of the MeSH tree:

  • Kale is Brassica
  • Sweet potato is Ipomoea batatas
  • Plum is Prunus domestica
  • Almond is Prunus dulcis
  • Apple is Malus
  • Cranberry is Vaccinium macrocarpon
  • Strawberry is Fragaria
  • Kidney Beans is Phaseolus
  • Chocolate is Cacao
  • Turmeric is Curcuma

If you’re searching for specific food plants, the Latin MeSH terms are usually not a problem, because when you search 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 explosion 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).

If you’re interested in learning about how to search for PBFs in PubMed, see our companion article, which includes an updated “search recipe,” or hedge.

[Image above is public domain, from WikiMedia]

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US Lags Behind The World In Plant-Based Food Research

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 charts below show our data for all PBFs and for 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.]


Image 1. Percentage of countrys’ total articles in PubMed that are on Plant-based food

PubMed search strategy used to find plant-based foods in chart above is described here.



Image 2. Percentage of countrys’ total articles in PubMed that are on Cabbage



Image 3. Percentage of countrys’ total articles in PubMed that are on Nuts



Image 4. Percentage of countrys’ total articles in PubMed that are on Fruit



Image 5. Percentage of countrys’ total articles in PubMed that are on Spices

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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.


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.).


Image 1. Almonds



Image 2. Walnuts



Image 3. Hazelnuts



Image 4. Cashews



Image 5. Pecans



Image 6. Brazil Nuts


Peanuts Are Different!


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

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


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 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 [mh:noexp] 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.

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Food, Diet & Nutrition – How To Search in PubMed


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.

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Searching for Food, Diet & Nutrition in PubMed Just Got A Lot Easier!

By Eric Rumsey, Janna Lawrence and Xiaomei Gu

As we’ve written earlier, the way that nutrition, food and diet subjects have been arranged in the MeSH tree explosion system has made it tricky to do comprehensive, all-inclusive searching. This has been the case because the three subjects have been in different places in the MeSH tree structure, so that each of them had to be searched separately, and then combined together to cover the subject. It’s likely that many people have searched only for “nutrition,” since that seems to them like the most general term to cover the field. By doing this, however, they have been missing citations on “food” and “diet,” which actually are much larger explosions in the MeSH tree structure than “nutrition.”

We are happy to report that the newly released MeSH changes for 2016 do have a new explosion that goes a long way to fixing the problem:

Diet, Food, and Nutrition [MeSH page]
… Beverages +
… Food +
… Nutritional Physiological Phenomena +
… … Diet+

This is a great advance! It’s no longer necessary to search nutrition, food and diet subjects because they’re now together in the new explosion –  Click here to see the results of  a search of the new explosion.

There are still a few nutrition-food-diet subjects that the new MeSH explosion does not cover (that are included in our hedge) but for most we recommend the new explosion highly!

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Searching Nutrition In PubMed & Embase: The Winner Is…

By Eric Rumsey and Janna Lawrence

As we’ve discussed, the big problem in searching for food-diet-nutrition subjects in PubMed is that the subjects are not together in a convenient bundle, as most subject groupings are in PubMed. To get a list of articles that includes food, diet and nutrition, it’s necessary to search each of these areas separately and then bundle them together into one search set.

When we first wrote about the difficulty of searching food-diet-nutrition in PubMed in 2013, we stated clearly that much of problem is caused by the fragmentation of the the relevant MeSH terms. So, jump forward a year. About two months ago, our library got institutional access to, sometimes called the “European MEDLINE.” Embase includes all of the articles in MEDLINE, as well as many other articles, and uses its own subject heading system. Because we’ve long been aware that food-diet-nutrition subjects are generally given more attention in Europe than in the US, we thought that the subject might get better treatment in Embase than it does in PubMed. We weren’t disappointed…

A Nutrition explosion that includes Food and Diet

Embase uses explosions to bundle related subjects together, much like PubMed, and, as we were hoping, it does indeed bring food, diet and nutrition subjects together in a convenient bundle. This is a great advance over PubMed. It becomes easy to combine a subject of interest with food-diet-nutrition, in one simple step. For example, using format:

‘Heart disease’/exp AND Nutrition/exp
Neoplasm/exp AND Nutrition/exp
‘Mental function’/exp AND Nutrition/exp

To do equivalent searches in PubMed, it’s necessary to do a hedge/filter search, such we have developed, or to search food-diet-nutrition terms separately and combine these with the subject of interest.

Better treatment of “Food” in Embase

Certainly having the inclusive food-diet-nutrition explosion is the biggest advantage in Embase. But there are other problems in PubMed, especially in the way the Food explosion is treated. In both Embase and PubMed, Food is the largest food-diet-nutrition explosion. There are several difficulties with this explosion in PubMed. An overall complication is that Food and Beverages have a confusing relationship. They are together in one explosion Food and beverages, which is made up of two separate explosions, one for each of the terms. If the user knows enough to search Food and beverages, he/she will get both terms. But if the user searches “Food,” the search will not include beverages. In Embase, beverage is an explosion that’s included in the food explosion, so searching “food” will retrieve articles on beverages.

Several other problems with the Food explosion in PubMed are caused by a lack of detail, in comparison with Embase. Some examples:

  • In PubMed, Fruit is not an explosion, although there are individual fruits included in the Plants explosion, usually under their Latin plant name. In Embase, the fruit explosion has 43 terms under it, 6 of which are themselves explosions.
  • In PubMed, Spices is an explosion with one term under it – Black Pepper. In Embase, the spice explosion has 31 terms listed under it, 4 of which are themselves explosions.
  • In PubMed, specific kinds of red meat, e.g. beef and pork, do not have their own MeSH terms; instead, they’re indexed under the general term Meat. In Embase, the meat explosion contains a red meat explosion, which has 7 terms, including beef and pork.

Related to the lack of detail in the Food explosion in PubMed is that many foods, especially plant-based foods, are not retrieved in a search for “food” because they don’t have specific terms in the Food explosion. We have written some “case studies” of this on chocolate, cranberries, and olive oil, all of which are in the Food explosion in Embase, but not in PubMed. We have also written an article on red meat being difficult to search in PubMed because there is no MeSH term for it; as mentioned above, Embase does have a term for it.

Looking at articles in Embase and PubMed that mention specific foods in the article abstract, it’s almost always the case that Embase’s detailed indexing will include descriptor terms for the specific foods, and PubMed usually will not. Comparison of article indexing is easy to do because Embase provides a “Source” filter, that makes it possible to limit to articles that are included in both Embase and PubMed. Each of the articles retrieved using this filter has a direct link to the citation in PubMed.

PubMed Advantages

The biggest advantage of PubMed, of course, is that it’s free to world. Embase, on the other hand, is an Elsevier product and is only available at institutions that have a subscription.

Another PubMed advantage is its simple Google-like interface, which is certainly more comfortable to most people. Embase uses an older style of interface that may appeal to librarians more than to most users. For anyone with a serious interest in food-diet-nutrition, though, we would say it’s definitely worth learning.

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Plant-Based Foods – An Inclusive PubMed Search

By Eric Rumsey and Janna Lawrence

In our earlier article on searching for plant-based foods (PBF) in PubMed, we suggested that a quick way to search the subject is to combine the MeSH Plants explosion AND our Food-Diet-Nutrition (FDN) hedge. This works quite well, especially for citations after 2002. In that year the Plants explosion was greatly expanded by the addition of several hundred new MeSH plant names. Before that, articles on specific plants were indexed inconsistently. Sometimes they were put under the plant family name, in which case they were included in the Plants explosion, and in other cases they were indexed under other terms like Vegetables, Fruit, or Plants, Edible, that are not in the Plants explosion.

In order to do the most inclusive search for plant-based foods, including citations before 2002, we have created two hedges, to be used for all the years in PubMed. These hedges include other MeSH terms and text-words, to supplement the plant-name search strategy that works well after 2002. We have done fairly thorough testing of the two hedges, and we recommend the first hedge for most searches. It uses MeSH terms, and it emphasizes “precision,” which means that it gets somewhat fewer citations, but the citations are more likely to be on target. For both of the hedges, we’ve combined them in an OR search with the simple “Plants AND FDN” hedge search mentioned above.

Here’s the first hedge, with the newly added terms in boldface:

(Vegetables [mesh] OR Fruit [mesh] OR Cereals [mesh] OR Plants, Edible [mesh] OR Soybeans [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 (Plants [mesh] AND (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))

[Number of citations, 8.19.14 - 265,126]

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.

Commentary on terms in this hedge (If the “Year introduced” is not given, the term has been in MeSH since its launch in 1966):

  • Vegetables [mesh]
    Citations: 84411
    An explosion that includes about 25 specific vegetables, including Onions, Soybeans, Daucus carota, and Solanum tuberosum. This is a relatively small proportion of all vegetables, which are indexed with their species or family name, in the Plants explosion.
  • Fruit [mesh]
    Citations: 57179
    Notably, this is NOT an explosion. All particular fruit types are indexed with their species or family name, in the Plants explosion.
  • Cereals [mesh]
    Citations: 73516
    An explosion that includes 8 cereals, including Avena sativa, Triticum and Zea mays. This is an important group, since it includes the world’s staple foods–wheat, rice, and corn.
  • Plants, Edible [mesh]
    Citations: 38945
    An explosion that includes several terms elsewhere in this hedge that get more citations when they’re searched separately. The term Plants, Edible by itself gets 5402 citations.
  • Soybeans [mesh]
    Year introduced: 1986
    Citations: 19284
    An explosion that includes Soy Foods, Soy Milk, and Soybean Proteins.
  • Dietary Fiber [mesh]
    Year introduced: 1982(1977)
    Citations: 13468
  • Flour [mesh]
    Citations: 3570
  • Bread [mesh]
    Citations: 3115
  • Diet, Vegetarian [mesh]
    Year introduced: 2003(1963)
    Citations: 2537
  • Nuts [mesh]
    Citations: 2074
  • Condiments [mesh]
    Citations: 1945
    An explosion that includes Spices.
  • Vegetable Proteins [mesh]
    Year introduced: 1975
    Citations: 1515

Here’s the second hedge, with the newly added terms in boldface:

(fruit OR fruits OR vegetable OR vegetables OR cereal OR cereals OR spices OR condiments OR flour OR nut OR nuts OR vegetarian OR soy OR soybean OR soybeans OR bread) OR (Plants [mesh] AND (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))

[Number of citations, 8.19.14 - 332,351]

To use this search, click this link, or see instructions above with first hedge.

Most of the words used in this hedge are text-word versions of the MeSH terms used in the first hedge. Since this emphasizes “recall” instead of “precision,” it gets more citations than the first hedge. But the citations are less likely to be relevant. We looked closely at citations using the two hedges, and it was easy to see the lesser relevancy of the citations in the second hedge. Most of these, of course, are retrieved because they mention words that are in the abstract (e.g. fruit, vegetables) but which are not assigned as MeSH terms.

A word about searching for older citations

When we first realized that most of the plant name MeSH terms were only introduced in 2002, it seemed like a serious problem. However, as we’ve looked back retrospectively, we’ve come to see that there really wasn’t much research attention given to the subject in the earlier days of MEDLINE, especially before about 1990.

We’ve done detailed work to study this, but in this article we’ll just give a couple of anecdotal examples of what we’ve found. We looked at the number of citations that contain the word “fruit” since 1968, and found that this stayed flat, at about 400 mentions per year, until about 1990. It’s grown fast since then, and in 2013, the word is in about 8000 citations. In another example, we found that there are 70 articles in all of PubMed that have “sweet potato” in the title, and are on human subjects. All but three of these are after 1992; zero citations from 1980-1992 contain the words in the title. So, if it seems like the hedges in this article aren’t finding many citations before 1990, it’s probably because there just aren’t many to be found.

Things improve in the 1990s. It appears, from our retrospective examination of citations on FDN, that as the volume of research on the subject increased, NLM gradually improved the quality of MeSH indexing to accommodate it. The coverage of more prominent plant families improved, and the application of existing FDN MeSH terms became more consistent. So in the 1990s, even before the mass introduction of new MeSH plant terms in 2002, FDN indexing and retrieval was improving.

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PubMed Food Problem: Red Meat

By Eric Rumsey and Janna Lawrence

As we’ve discussed before, searching for “red meat” in PubMed is difficult because the subject is poorly covered in the MeSH vocabulary. Not only is there not a term for “red meat,” but there are also no MeSH terms for specific kinds of red meat (beef, pork, etc.). There is only the one all-inclusive MeSH term Meat, which includes all kinds of meat, as well as fish and poultry. So this is a rare case in PubMed in which MeSH is essentially useless. The only way to do a thorough search is to use text words that include the phrase “red meat” or that contain specific types of red meat – e.g. “red meat” OR beef OR pork… [etc]

The problem of searching for red meat has returned to our attention recently for two reasons. One is that the subject continues to be in the news. Last winter when we wrote, it was getting attention because red-meat nutrient carnitine was reported to be linked to heart disease. And recently red meat has been back in the news because it’s been reported that tick bites can trigger an allergy to red meats.

The other reason we’ve been thinking about red meat is that, coincidentally, our library has recently gotten a subscription to Embase, which a European-based medical literature database that’s the main alternative to PubMed/MEDLINE. Of course, the first thing we did with new access was to compare the indexing, and especially the explosions, in Embase to PubMed for FDN subjects. We have found several cases in which Embase is better. One case in which it’s clearly better is red meat.

Here’s the explosion in Embase:

Red Meat
… Beef
… Lamb Meat
… Mutton
… Pork
… Rabbit Meat
… Veal
… Venison

This can’t be used directly in PubMed, of course, but at least it gives and idea of specific meats to search in PubMed as text words.

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