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Nutrition in Clinical PracticeLindsey and Olin 2013
NCPXXX10.1177/0884533613475821
Invited Review
Nutrition in Clinical Practice Volume XX Number X Month 2013 1-12 2013 American Society for Parenteral and Enteral Nutrition DOI: 10.1177/0884533613475821 ncp.sagepub.com hosted at online.sagepub.com
Abstract
PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed databases structure and features as well as strategies for conducting an effective search. (Nutr Clin Pract. XXXX;xx:xx-xx)
Keywords
PubMed; MEDLINE; National Library of Medicine; search strategy; National Center for Biotechnology Information
PubMed (www.PubMed.gov) is a biomedical and life sciences database that was created and is currently maintained by the National Center for Biotechnology Information (NCBI), which is a division of the National Library of Medicine (NLM).1 It is available free of charge on the Internet, with numerous journals allowing free full-text access to articles retrieved. It may also be accessed using free apps on mobile devices, such as PubMed on Tap, Pubmed4Hh, and Unbound MEDLINE. In 2011, PubMed indexed 991,618 articles and, as of this writing, contains more than 22 million total citations.2 To be included in the database, a PubMed selection committee scores each submitted title with a maximum possible score of 5 based on the quality of the research and clinical importance. Journals that score at least 3.75 are selected for indexing. PubMed includes information from several different sources such as life science articles indexed in MEDLINE, additional out-of-scope citations from general science and chemistry journals, life science journals that submit full-text articles to PubMed Central, and the NCBI Bookshelf collection, which includes over 1000 book titles.1 An example of a title from the NCBI Bookshelf that readers may find useful when unsure how to cite a particular reference is Citing Medicine: The NLM Style Guide for Authors, Editors, and Publishers, by Patrias and Wendling.3 MEDLINE comprises the largest portion of PubMed (approximately 90%), and according to the NLM, MEDLINE indexes about 20%25% of all new biomedical titles reviewed.4,5 The NLM also estimates that there are between 13,000 and 14,000 journal titles published worldwide, and MEDLINE indexes 5619 of these titles. MEDLINE has indexed a greater number of articles every year than the year prior and, based on numbers for 2011, trended toward indexing
1,000,000 articles in 2012. Although there are likely many other articles published each year as well, these 1 million articles will represent, based on NLM standards, the new and clinically relevant articles published for the year. A significant number of articles are not indexed, but these have been deemed less useful by the PubMed selection committee. A recent area of information access research involves comparing PubMed with other popular medical literature search engines, in particular Google Scholar. In general, these studies show that both programs return similar numbers of citations and resources; however, PubMed references tend to be more specific for the intended topic.6-9 Google Scholar searches provide a greater variety of references that include books, websites, and other Internet-based resources, but these references are typically less applicable to the intended search. Previous articles have addressed searching PubMed and highlighted different features of the resource; however, new search language options, filters, and features have been incorporated.10-13 The objective of this article is to provide the clinician an overview of PubMeds current structure and features as well as basic guidance for conducting an effective literature search.
From the Drug Information and Learning Resource Center, Harrison School of Pharmacy, Auburn University, Auburn, Alabama. Financial support: None declared. Corresponding Author: Wesley T. Lindsey, PharmD, Drug Information and Learning Resource Center, Harrison School of Pharmacy, Auburn University, 1311 Walker Building, Auburn, AL 36849, USA. Email: wtl0001@auburn.edu.
Figure 2. Once a saved search has been created, an option is available under the My NCBI homepage, where the system will automatically rerun and update the search and e-mail new citations to a preferred e-mail on a monthly, weekly, or daily schedule. To activate this feature, click on the My NCBI homepage link while logged in and look under the box titled Saved Searches. There is a small gear icon immediately to the right of the search terms. Clicking on this icon will access the Saved Search Settings page, which then allows for setting the frequency of updated searches, the format they can be provided in (Summary, Abstract, or MEDLINE), and the maximum number of citations that should be sent at one time. If the clinician elects not to have new citations provided over e-mail, a feature is available in the Saved Searches box titled Whats New. This feature automatically updates the search and provides the number of citations that have been added using the parameters stated. By clicking on the number below the Whats New title, the latest citations will be provided. Establishing a user account will also allow the clinician to create Collections of citations for several purposes. The Collections feature is available in the My NCBI homepage after the user is logged in. The default available options listed in the Collections box are My Bibliography, Favorites, and Other Citations. The My Bibliography feature is intended for the clinician to create a list of his or her authored works and citations. Citations may be drawn from the PubMed database or can be entered manually if the reference is not indexed. The My Bibliography list can be kept as a private feature, may be shared publicly, and may be downloaded into a reference citation manager program. The Favorites collection is
intended to act as a repository of favorite citations of the user. The Other Citations collection is identified as a place to permanently store citations contributed to but where the clinician is not an author; however, it may be used for the preferred purpose of the clinician. A virtually unlimited number of additional collections can be created by the user. This can be done by performing a literature search in PubMed while logged into the My NCBI feature, identifying the important citations that need to be kept or cataloged, and clicking on the Send To feature identified in Figure 2. By clicking on this link, several options are presented and the user should highlight the button next to Collections. Once the button is filled, a new option will generate directly underneath asking to confirm to Add to Collections. By clicking on the Add to Collections link, the user will be taken to a new screen, where he or she is presented the option of placing the citations in an existing collection through a drop-down menu or creating a new collection. When Create New Collection is selected, the option appears to title the new collection, which will then be created once the title is entered into the text box and the Save button is clicked. A final feature of the My NCBI homepage is the Recent Activity box. This feature will save all searches and activities of the user for 6 months as long as the activity is performed while logged in and the search is not saved using the Save Search process described above. Clicking on an active link beside the activity will rerun that action with updates; for example, a search for a specific author performed 4 months ago can be rerun by clicking on the blue link out to the side with any new citations being provided in the updated search.
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Table 1. MeSH Vocabulary Main Branches in PubMed. Anatomy Organisms Diseases Chemical and Drugs Analytical, Diagnostic and Therapeutic Techniques and Equipment Psychiatry and Psychology Biological Sciences Natural Sciences Anthropology, Education, Sociology and Social Phenomena Technology, Industry, Agriculture Humanities Information Science Named Groups Health Care Publication Characteristics Geographic Locations
MeSH, medical subject headings.
PubMed will be automatically mapped to the MeSH database, and the matching terms will be presented and searched.19 This may or may not result in an effective or efficient search.
As mentioned earlier, there are 26,853 Descriptor records in the MeSH database, and these are reviewed (and generally grow) annually. There are relatively few Qualifiers, 83, and these are used in conjunction with the Descriptors. As the term implies, the Qualifiers lend specificity and definition to broader terms and can be used with multiple Descriptors. SCRs are used to index chemicals, drugs, and a few other concepts (eg, rare diseases). The SCRs are also linked to Descriptors and are generally broader; there are manyover 200,000 records and these are updated weekly.17 The NLM staff examines articles and assigns the best, most specific MeSH headings that describe the concepts discussed in the article. The indexer may assign as many MeSH headings as appropriate to cover the topics of the article, but this generally ranges from 515 headings. When there appears to be no existing heading for a concept, the indexer will use the closest, general heading available, and Subheadings may also be assigned to more specifically describe an aspect of a MeSH concept. Using the MeSH terms to search PubMed will generally be the most efficient pathway to locating the desired information of the literature search. Therefore, the NLM has created the MeSH Browser to help locate the most appropriate vocabulary terms for the topic.18 The browser is intended only to help narrow the search terms. It includes various other information, including annotations, history notes, and allowable qualifiers; however, it does not link directly to MEDLINE or other database retrieval systems. The search can be limited to any or all of the main sections of the MeSH headings (Descriptors, Qualifiers, SCRs). Remember also that when PubMed searches a MeSH term, it will automatically include narrower terms in the search where applicable. This is called the automatic explosion. The MeSH Browser is accessed from the PubMed home page (http://www.ncbi.nlm.nih.gov/PubMed) from the link MeSH Database and then from the link NLM MeSH Homepage. It is not required to use specific MeSH terms for searching. Any term that is typed into the search box of
There are times when PubMed is unable to match a search term with the MeSH, journals, author or investigator tables, or indexes. PubMed will then search the individual words in All Fields, and the individual terms will then be combined (ANDed) together. A spell check feature suggests alternative spellings for search terms that include misspellings. Results from a search with the closest common word will display, or an option to link to an alternative spelling. Note that alternative spellings are based on the frequency of use in PubMed and not a dictionary, so the offered choice may not be appropriate. Exceptions include terms with numbers or fewer than 5 characters. It works best for terms with multiple words. Related Citations is just that. PubMed will provide citations similar to the ones retrieved by using a combination of the MeSH headings and a word-weighted algorithm to compare words from the Title and Abstract of each citation. The Related Citations display is in rank order from most to least relevant in the search results screen. The linked citation is displayed first.
only the most current literature is appropriate or anything less than 5 years old. This is strictly dependent on the question being asked, and occasionally, dated material is most appropriate. Species. This limits to studies of humans or other animals. Depending on the topic, it can be surprising how many animal studies will be available; if your focus is humans, it is a useful filter. If both options are checked, you will get both. Article (publication) types. This is used to retrieve very specific types of publicationsfor example, Clinical Trial, Meta-Analyses, Practice Guidelines, or Systematic Reviews. A common use of literature retrieval is to find recent reviews on topics, rather than exhaustive searches for all literature, and this option is extremely useful. The default options are frequently searched publication types. Multiple selections are allowed. Languages. PubMed indexes journals published in about 40 languages. English is the default language; click more . . . to view and select from an alphabetical list of all available languages. Many articles published in a foreign language have an English abstract. Journal categories. Click Show additional filters to find and display the journal categories, then check Journal categories. Journal categories are citations from lists of journals indexed in MEDLINE with additional relevant citations. Click on 1 of the 4 choices and your search results will be displayed using only that category of journal. The 4 journal categories are as follows: Core clinical journals Dental journals MEDLINE Nursing journals Ages. Click Show additional filters to find and display the age group filters. Check the desired filter to activate. The age groups displayed are self-explanatory and allow one to further focus a search as appropriate. Up to 14 age groups are available; select more . . . to see additional age groups. Multiple choices are allowed. This may be most useful when searching for clinical trials in specific patient populations.
Filters
The use of filters is a great way to narrow your search results and is integral to a successful and efficient search. Filter options appear to the left of the results (see Figure 2). Simply click on a filter to apply it to your search; multiple selections are allowed. Once chosen, the active Filters appear above your search results. To discard a filter, click the filter name again. Only the more common filters display by default. Click Show additional filters to view additional options. All filters can be cleared by clicking Clear All. The choice of filters will also depend on the results retrieved. For example, Clinical Trials will not be a choice in results devoid of clinical trials. Some of the more useful filters are discussed here. Text availability Abstract available: The record includes an abstract. This usually restricts your search to records dated after 1975. Free full text available: The record has a link to a freely available copy of the full-text article. Full text available: The record has a link to the full-text article. Both free full text and full text are very useful, but use them judiciously; restricting a search to full text only may severely limit the results obtained. Publication dates. PubMed contains citations published back to 1946 and earlier, but any date range can be set depending on search needs; the narrower the date range, the fewer citations retrieved. Ranges for 5 years and 10 years are given and are the most common selections. A custom range can specify a date range using year, month, and day if that specificity is needed, but the month and day are optional. PubMed displays search results in descending date of entry orderthat is, last in, first out. A common misconception in literature retrieval is that
Building Blocks
In the context of database searching, Boolean logic refers to the logical combinatorial relationships among entitiesin this case, search terms.20 The common Boolean operators AND, OR, NOT are used to combine search terms. The Boolean operators must be entered in uppercase letters. AND: Using AND between terms is asking the search engine to find articles that contain both the terms; articles containing either term, but not both, will not
be captured. Also, AND is the default operator used in PubMed. If you do not include Boolean operators in your search string, AND will automatically be inserted between terms. OR: Used to combine terms/concepts. If one term has 10 articles and a second term has 20 documents, your result will list approximately 30 documents. NOT: Use this term to eliminate a term/concept from the search. For example, searching for information on nutrition in American football players, a possible search string would be Nutrition AND football NOT soccer. Use the most caution with the NOT operator as it is easy to eliminate relevant articles. Multiple Boolean operators in PubMed are processed left to right. For example, nutrition AND football OR injuries. This will retrieve records that include both nutrition AND football as well as all records with the term injuries, whether or not they contain the other 2 terms. Nesting is used to change the processing order of the terms, and parentheses are used to create the desired order. The terms inside the set of parentheses will be processed as a unit (the nest) and then incorporated into the overall strategy. For example: nutrition AND (football OR injuries). This will retrieve records for nutrition, as well as one or both of the terms football OR injuries.
Search by Citation
Sometimes, the search consists of finding a specific article with all or pieces of the citation. To find a specific citation using citation elements, simply type the available information into the Search Box. Citation Sensor assists searchers looking for a specific article. It looks for combinations of search terms that are characteristic of citation searching (eg, volume/issue numbers, author names, journal titles, publication dates). If the search invokes the Citation Sensor, you will see a yellow area above the default retrieval with links to one or more citations for your consideration. The citation needs to be accurate to avoid too many choices. Single Citation Matcher is available from the PubMed Home page and the Advanced Search page. It is a form with spaces about elements of a citation (eg, author, title, journal, volume, issue, page) by field. It is preferred over the Search Box approach.
Display Settings
To view the full display of a record in PubMed, click on the title link. Use the Display Settings menu to change the display format, the number of citations per page, and the sort order of your results. Change your default display settings using My NCBI Preferences. There are many choices for display formats. If a great deal of quality time will be spent with PubMed, these are worth investigating.
History
Your PubMed Search History is available on the Advanced Search page, just under the Search Box. This page shows your search strategies and number of items found for each search and when it was run. Individual searches can be combined with each other or with new search terms using Boolean logic. To build other searches from previous ones, click Add and the search will go above to the Search Box. It then defaults to the Boolean AND, to combine with another previous search term, added in the same way as the first. In some ways, this is a more systematic approach to searching, that is, to search single terms/phrases based on the search question, observe the result, and then combine the terms using the Boolean operators stepwise. This may help in obtaining all desired articles by avoiding messy logic statements using more than one Boolean operator. History can hold a maximum of 100 search statements. Once that number is reached, searches will be removed, beginning with the oldest search first.
Truncation
Truncation can be used when you want PubMed to find all terms that begin with a given text string. Truncation is represented by the asterisk (*), also known as a wildcard. For example, a search is required for all forms of the root nutrition. If you search nutrition*, PubMed will retrieve words such as nutrition, nutritional, nutritionist, and so on. However, PubMed restricts retrieval to the first 600 variations; once exceeded, a warning message will display. Also, truncation turns off automatic term mapping and the automatic explosion of MeSH terms.
The Systematic Reviews portion of Clinical Queries functions, as the name implies, to search for literature on the intended topic that is categorized as a systematic review, metaanalysis, conference consensus statement, or clinical practice guideline. This feature is similar to performing a literature search from the main PubMed screen and then applying the appropriate filters on the left side of the screen; however, this feature applies the filters proactively instead of retroactively. If the user is intentionally searching for review articles or guidelines, it may be more efficient to use this feature. The Journals Database feature is accessible from the main PubMed search page and is highlighted in Figure 1. This portion of PubMed allows the user to search for journals that are currently or have previously been indexed as part of MEDLINE or the other NCBI databases. Clinicians can enter search terms in the Search Box that include a topic, the name of a specific journal, or the International Standard Serial Numbers (ISSN). Searching for journals such as Nutrition in Clinical Practice will provide the user numerous journal features such as official NLM abbreviation, publication frequency, MEDLINE indexing history, start date of publication, and if the journal has been subject to name changes.
has been created through My NCBI (as described above), all of the collection may be exported by selecting none of the individual citations, or select citations can be identified using the checkboxes located directly above the citation number. Finally, citations that have been selected and sent to a Clipboard may be exported. The process for exportation is identified in Figure 4. Note: If using Endnote as your reference manager, you will be asked to identify a location to send and save the resulting file. Also, Endnote may automatically start and request to identify an export filter. PubMed is an available option on the scroll-down menu and should be selected when exporting from PubMed.
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The results may be further limited by choosing selected filters on the left margin. For simplicity, select Publication dates of the past 5 years (5 years), Species of Humans, and Language of English. Each filter will further narrow the search, resulting in a final list of 7 articles. As discussed in the text, the last choice in the left column is Show additional filters. This provides more choices to limit the search if desired, such as sex, subject age, journal types, and so on, as seen in Figure 10. Alternatively, one could type in as a single search prealbumin and nitrogen balance, and in this case, the results are the same. In other cases, particularly if the combined search combinations become more complex, results may be different.
References
1. PubMed Help. Bethesda, MD: National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/books/NBK3827/. Updated August 8, 2012. 2. Corlan AD. Medline trend: automated yearly statistics of PubMed results for any query, 2004. http://dan.corlan.net/medline-trend.html. Updated February 14, 2012. 3. Patrias K, Wendling D. Citing Medicine: The NLM Style Guide for Authors, Editors, and Publishers. 2nd ed. Bethesda, MD: National Library of Medicine; 2007. http://www.ncbi.nlm.nih.gov/books/NBK7256/ 4. FAQ: journal selection for Medline indexing at NLM. http://www.nlm. nih.gov/pubs/factsheets/j_sel_faq.html#a15. Updated January 6, 2012. 5. Searching PubMed with MeSH. Bethesda, MD: U.S. National Library of Medicine, National Institutes of Health. http://www.nnlm.gov/training/ resources/meshtri/pdf. Updated May 2012. Accessed September 28, 2012. 6. Falagas ME, Pitsouni EI, Malietzis GA, Pappas G. Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses. FASEB J. 2008;22:1-5. 7. Shultz M. Comparing test searches in PubMed and Google Scholar. J Med Libr Assoc. 2007;95(4):442-445. 8. Freeman MK, Lauderdale SA, Kendrach MG, Woolley TW. Google Scholar versus PubMed in locating primary literature to answer drugrelated questions. Ann Pharmacother. 2009;43:478-484. 9. Anders ME, Evans DP. Comparison of PubMed and Google Scholar literature searches. Respir Care. 2010;55(5):578-583.
Conclusion
PubMed is an extremely useful tool for clinicians seeking the most up-to-date clinical information for practice or research. As with any piece of technology, the features and functionalities of PubMed are constantly evolving. Newer features of PubMed include the ability to search more natural language terms instead of only MeSH headings, customize the user experience through the My NCBI portal, incorporate predetermined filters into the Clinical Queries feature, and support academic projects by allowing exportation to reference manager programs.
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10. Schrimsher RH, Kendrach MG. A primer: basic PubMed searching for pharmacists. Hosp Pharm. 2006;41(9):855-867. 11. Dupras DM, Ebbert JO. Clinicians guide to new tools and features of PubMed. Mayo Clin Proc. 2007;82(4):480-484. 12. Sood A, Erwin PJ, Ebbert JO. Using advanced search tools on PubMed for citation retrieval. Mayo Clin Proc. 2004;79(10):1295-1300. 13. Ebbert JO, Dupras DM, Erwin PJ. Search the medical literature using PubMed: a tutorial. Mayo Clin Proc. 2003;78:87-91. 14. The Free Dictionary by Farlex. Huntingdon Valley, PA: Farlex; 2012. http://medical-dictionary.thefreedictionary.com/Controlled+vocabulary. Accessed September 27, 2012. 15. Fact sheet: Medical Subject Headings (MeSH). Bethesda, MD: U.S. National Library of Medicine, National Institutes of Health. http://www. nlm.nih.gov/pubs/factsheets/mesh.html. Updated August 29, 2012. Accessed September 28, 2012. 16. Medical Subject Headings: preface. Bethesda, MD: U.S. National Library of Medicine, National Institutes of Health. http://www.nlm.nih.gov/mesh/
intro_preface.html#pref_rem. Updated August 27, 2012. Accessed September 28, 2012. 17. Medical Subject Headings: MeSH record types. Bethesda, MD: U.S. National Library of Medicine, National Institutes of Health. http://www. nlm.nih.gov/mesh/intro_record_types.html. Updated August 30, 2012. Accessed September 28, 2012. 18. Medical Subject Headings: MeSH browser. Bethesda, MD: U.S. National Library of Medicine, National Institutes of Health. http://www.nlm.nih. gov/mesh/mbintro.html. Updated August 31, 2012. Accessed September 28, 2012. 19. Canese K, Jentsch J, Myers C. PubMed: the bibliographic database. In: McEntyre J, Ostell J, eds. The NCBI Handbook . Bethesda, MD: National Center for Biotechnology Information; 2002. http:// www.ncbi.nlm.nih.gov/books/NBK21101/. Updated August 13, 2003. 20. Merriam-Webster Dictionary. http://www.merriam-webster.com/diction ary/boolean. Accessed October 1, 2012.