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New Resource: InCites

By
Jennifer DeBerg
– May 4, 2017Posted in: Library Resource

The UI Libraries recently obtained a license to InCites, a citation-based evaluation tool for academic and government administrators to analyze institutional productivity and benchmark output against peers in a national or international context. This resource enables rapid generation of reports, as it utilizes data from the Web of Science indexes already part of the UI Libraries collection. Below is a screenshot of the categories of reports available.

Includes people, organizations, regions, research areas, journals/books/conference proceedings, and funding agencies

 

 

InCites is available from the UI Libraries Databases A-Z list. In order to access this resource, an account is required. A previously created Web of Science account can be used or a new account can be created at the top right side of screen. If this resource is of interest to you, consider viewing additional training resources.

Please contact your subject librarian or the Hardin Library Reference desk with problems or questions.

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New Journal Metric: CiteScore

By
Jennifer DeBerg
– January 30, 2017Posted in: Library Resource

Scopus, a multi-disciplinary literature database, has recently launched CiteScore metrics for titles that publish on a regular basis, such as journals and other serial publications. The CiteScore was developed as another tool for analyzing the importance of journals, similar to the Journal Impact Factor originally developed by the Institute for Scientific Information and now available in Journal Citation Reports (JCR) through the Web of Science database.

The Cite Score is calculated by dividing number of citations received in a calendar year by all items published in the journal in the preceding three years. This is similar to how the Journal Impact Factor (JIF) is calculated, with a few major differences: 1.The JIF is calculated by measuring the preceding 2 years, as compared with 3 years for the CiteScore 2. CiteScore is less selective about how it determines citable items, and will include records with potential for citations (including letters to editor, news pieces) whereas the JIF only includes records that are most likely to draw citations, such as research papers 3. Access to CiteScore is freely available, whereas JCR requires a subscription. See a detailed FAQ page or more information.

In order to try out this new tool, select the Sources tab upon access of Scopus, as pictured below. If there are questions about this or other Hardin Library resources, please contact our reference desk or follow up with the appropriate subject librarian.

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PubMed Food Problem: Cranberry & Cranberries | Update

By
Eric Rumsey
– December 6, 2016Posted in: Nutrition, Plant-Based Foods, PubMed

cranberry700x350

Because most plant-based foods are under “plants” instead of “food” in PubMed, articles on cranberries may not be retrieved in a search for Food.

By Eric Rumsey, Janna Lawrence and Xiaomei Gu

Part of the problem in searching for food in PubMed is that it’s often the case that there’s a fuzzy border between between food and medicine.   A food that is enjoyed for its taste and general nutritional benefits may have properties that make it therapeutic for specific health conditions. A good example of this is cranberries, and cranberry juice, which may have benefits for prevention of urinary tract infections.

As with most plant-based foods, in MeSH indexing, cranberry is in the Plants explosion, and it’s not in the Diet, Food, and Nutrition explosion. Fortunately, most articles on cranberries and cranberry juice are assigned some Diet, Food, and Nutrition indexing terms so that they are retrieved in searches for the explosion. For instance, articles on cranberry juice are often under Beverages, and some articles on cranberries are under Fruit or Dietary supplements. However, there is still a significant number of relevant articles on the subject that are missed.

To show examples of cranberry-related articles that are not retrieved by the Diet, Food, and Nutrition explosion, we searched for cranberry or cranberries in the article title, limited to human, and retrieved 391 articles. We then combined this with the Diet, Food, and Nutrition explosion. This retrieved 269 articles — 69% of the cranberry/cranberries articles, which is a fairly good retrieval. But still, it’s certainly notable that there are 122 articles that are not retrieved, many of which appear to be very much on target, that don’t contain any Diet, Food, and Nutrition MeSH terms. Here are some examples:

As we mentioned above, plant-based foods are tricky to search in PubMed because the name of the food plant is usually only in Plants, and not in any FDN explosion. The six articles above are all indexed under Vaccinium macrocarpon, the taxonomic name of cranberry, which is in the Plants explosion. So if you were searching for articles on urinary tract infections and plant-based foods, a strategy that would retrieve these articles would be to combine Urinary Tract Infections AND Plants.

The image at the top of the article is original.

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PubMed Food Problem: Cruciferous Vegetables

By
Eric Rumsey
– December 1, 2016Posted in: Nutrition, Plant-Based Foods, PubMed, Uncategorized

cruciferousvegetables_690x345

To do a PubMed search for cruciferous vegetables that includes such species as Radish and Arugula, each species must be done separately.

By Eric Rumsey, Janna Lawrence and Xiaomei Gu

In order to do successful searches for cruciferous vegetables in PubMed, it helps to know exactly what “cruciferous” means, which makes it easier to understand what vegetables are considered “cruciferous” and the botanical relationships among them. We have discussed these topics in a companion article.

In general, cruciferous vegetables are considered to be any plants in the family Brassicaceae that are edible. Most of these, especially the more popular ones (cabbage, broccoli, cauliflower, brussel sprouts) are in the genus Brassica. A few others are in other genera in the family, the most notable being Radish (Raphanus), Daikon (Raphanus), Arugula (Eruca), Horseradish (Armoracia), White mustard (Sinapis), Garden cress (Lepidium) and Wasabi (Wasabia). With most edible members of the family Brassicaceae being in the genus Brassica, then, searching for that genus works well for most cruciferous vegetables. But without including the MeSH terms for all of the other edible genera in the family, there is no easy way to do a comprehensive search for them as a group.

With edible species in several genera in the Brassicaceae family, it might seem like a way to include all of them would be to search for the family name, since it’s an explosion that contains all of the genera in the family. We have seen this done by MeSH indexers in some cases, but it has problems. For one thing, the family is very large, containing 372 genera, so searching for the family name can retrieve many inappropriate citations. This is especially a problem because one of the genera in the family is Arabidopsis, a very commonly used research subject in plant genetics, having nothing at all to do with nutrition. Arabidopsis is something like the Drosophila of the plant world. So of course searching for the exploded MeSH term Brassicaceae gets a flood of articles on Arabidopsis; approximately 80% of all articles retrieved from this search are indexed to the narrower term Arabidopsis.

We found another problem in how cruciferous vegetables are treated in PubMed indexing when we looked at sample of 30 articles with “cruciferous” in the title.  Twenty-eight of the 30 articles actually had the phrase “cruciferous vegetables” in the title, but  in about ⅓ of the 30 articles, there was no indexing term at all correlated with the word “cruciferous,” and the indexing term used was just “vegetables,” ignoring the word “cruciferous.” Another problem we found in this sample is that, of the articles that had an indexing term correlated with “cruciferous,” the term that was usually used was the family name, Brassicaceae, which retrieves many non-food-related citations, as discussed above.

Suggestions for improving indexing of cruciferous foods

Because there is currently no way to search for cruciferous foods as a group, we would suggest that NLM should add a new MeSH term <cruciferous foods>. This would not only put all of these foods under one term, it would also provide a term to use for articles that use the term itself in the title or abstract.

Image at top of article is from Wikipedia.

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The meaning of cruciferous

By
Eric Rumsey
– November 30, 2016Posted in: Nutrition, Plant-Based Foods

cruciferousflowers4

To modern ears, “cruciferous” is all about vegetables. But the word’s rich history shows that it was formerly used in a much broader sense.

By Eric Rumsey, Janna Lawrence and Xiaomei Gu

In a Google search for the word “cruciferous,“ 9 out of the top 10 retrievals contain the phrase “cruciferous vegetables.” This certainly does fit the predominant modern usage of the word. As a game show host might say, “what do you think of when I say ‘cruciferous’?” Well, of course, “vegetables”! But it hasn’t always been this way. As the Google Ngram chart below shows, the phrase “cruciferous vegetables” only came into prominent use about 1980. Before that, the word “cruciferous” was widely used in other contexts.

ngramcruciferousveg1110

To understand the real meaning of the word, it’s important to understand what these other contexts are. This is important for more than simply historic reasons; it’s also important to understand the meaning of the word to understand its connections to nutrition, and because it helps to search for the subject in databases such as PubMed (as we’ve discussed in a companion article). Additionally, it’s a surprisingly interesting story.

The key to understanding “cruciferous” is a knowledge of its rich botanical history. The chart below gives a hint of this. The chart is a comparison of the use of the words Cruciferae and Brassicaceae. These are names that have been assigned to the plant family that contains “cruciferous vegetables” and many other plants as well. As the chart indicates, Cruciferae was the name of the family until the early 20th century, when it was officially changed to Brassicaceae. Since then, botanists have gradually been switching the word they use, with continuing widespread use of the older name Cruciferae.

ngramcruciferaebrassicaceae1111

This seemingly arcane naming distinction is important because when the family name was Cruciferae, the word cruciferous was used to include all plants in the family, not just the edible species that we call “cruciferous vegetables,” which helps explain the common use of the word in the chart above. (Examples from Google Books of the broad botanical use of the word “cruciferous” in the 19th century are here, here, and here.) The significance of this is magnified by the fact that the family is very large, containing 372 genera and 4060 species, making it one of the largest flowering plant families. This and other details of the family are well-covered by a Wikipedia article on it. Another detail that gives an idea of the size and variety of the family and helps explain the widespread use of “cruciferous” is that, in addition to cruciferous vegetables, it also includes decorative flowers, weeds, and Arabidopsis thaliana (“a very important model organism in the study of the flowering plants”).

Relating to the image of three flowers at the top of the article, another help in understanding “cruciferous” is the etymology of the word itself. The word comes from the word “cross,” because the 4-petaled flowers have the appearance of a cross. The flowers in the image above are (from left) Raphanus sativus (Wild radish weed), Brassica oleracea (Broccoli) and Arabidopsis thaliana. (Images are from Wikipedia).

In conclusion, the word “cruciferous” is confusing because the word has its origins in a time when the large family Brassicaceae was called Cruciferae, which meant that all of the plants in the family (most of which are not edible) were referred to as “cruciferous.” In the last generation, as botanists have switched to calling the family Brassicaceae instead of Crucuferae, and as people have become more aware of nutrition, the word “cruciferous” has gradually come to be used most commonly in the context of “cruciferous vegetables.” As we’ll discuss in a companion article, it’s important to know about this history and the taxonomic relationships of cruciferous vegetables in order to do successful searches in research databases like PubMed.

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

By
Eric Rumsey
– October 19, 2016Posted in: Nutrition, Plant-Based Foods, PubMed

chocolatebgfffcrop3

Because most plant-based foods are under “plants” instead of “food” in PubMed, articles on chocolate may not be retrieved in a search for Food.

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:

Plants
   Angiosperms
      Sterculiaceae
         Cacao

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
http://www.ncbi.nlm.nih.gov/pubmed/1860135

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.

[Image above is licensed under Creative Commons, from WikiMedia]

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Google Scholar | Change settings to find full-text articles

By
Sarah Andrews
– October 14, 2016Posted in: Library Resource

In order to find full-text articles, please change some settings in Google Scholar.   This change is necessary due to the libraries moving to a new electronic management system called UILink.

  1. Please use the library link to Google Scholar, so you can be identified as a University of Iowa affiliate. 
    http://purl.lib.uiowa.edu/GoogleSch

  2. Click on Settings in Google Scholar.
    image of google scholar screen
  3. Select Library links and uncheck boxes under the search bar

    screen shot library links screen
  4. Type Iowa into the search bar and select The University of Iowa – ViewIt@UILink and Save
    googlescholar4
  5. After you complete a search in Google Scholar, you should see a results screen like this.  Click on ViewIt@UILink  to view full-text article.
    googlescholar5

If you need help, please contact Hardin Library or your campus library.

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Sign Up for an ORCID iD–Your Research Identifier

By
Sarah Andrews
– September 28, 2016Posted in: Technology

orcid1The UI Libraries, partnering with Information Technology Services, the Office of the Provost, the Division of Sponsored Programs, and the Big Ten Academic Alliance are leading an initiative to help all research active University of Iowa staff and faculty obtain an ORCID iD and/or link their existing identifier to their University of Iowa email address.

ORCID (Open Researcher and Contributor ID) is a non-profit, platform agnostic registry of unique author identifiers. Many publishers, funders and academic institutions have already adopted ORCID and may be requiring its use in the near future.

Having an ORCID iD

  • makes your work discoverable by others
  • connects your research to you throughout your career, no matter how your name appears in publication
  • distinguishes you from other researchers with similar names
  • minimizes the time you spend filling out forms when submitting research or applying for grants
  • is being required by major journal publishers and funders
  • gives you access to an ImpactStory page (an altmetrics tool)

Click the green button below to sign up for your ORCID iD (Iowa Hawk ID and password required)

greenbox1

 

 

To learn more about ORCiD at the UI, see the UI Libraries information page.

If you have any questions about ORCiD please contact your liaison.

Sample ORCID iD page

Sample ImpactStory

 

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