CONCISE NEW TOOLS AND REVIEW FEATURES OF FOR PUBMED CLINICIANS Clinicians Guide to New Tools and Features of PubMed DENISE M. DUPRAS, MD, PHD, AND JON O. EBBERT, MD, MSC Practicing clinicians need to have the skills required to obtain upto-date medical information to address both the expansion of scientific knowledge and patients increasing use of the Internet. PubMed (www.pubmed.gov) allows clinicians free access to the largest biomedical resource available. This article is the third in a Mayo Clinic Proceedings series designed specifically to help clinicians unlock the tools and information available through this valuable resource. Mayo Clin Proc. 2007;82(4):480-484 CAM = complementary and alternative medicine; NCBI = National Center for Biotechnology Information; NLM = National Library of Medicine The amount of medical information continues to increase at an exponential rate. Staying current with important advances in medicine remains a substantial challenge for busy practicing clinicians. Patients are increasingly using the Internet to find medical information as well. Consequently, clinicians are being faced with the additional challenge of reviewing information obtained by patients and seeking the best scientific evidence to guide patient care decisions. PubMed is a service of the US National Library of Medicine (NLM) and includes more than 16 million citations from the MEDLINE database and from other life science journal databases for biomedical articles dating back to the 1950s. PubMed is searched using Entrez, an integrated, text-based search and retrieval system used by the National Center for Biotechnology Information (NCBI) to search PubMed as well as genetic, protein, and taxonomy databases. The integrated nature of PubMed enables clinicians to easily access relevant journal articles that can be linked to other databases, online reference textbooks, and patient information. PubMed can be accessed from any computer with Internet access by typing the address www.pubmed.gov. Since our previous publications on the use of PubMed, 1,2 updates have occurred, and additional features have been added that further increase the usefulness of this free Internet-based resource. The purpose of this article is to help clinicians access and use these resources. For new users, PubMed offers online animated and user-friendly printable tutorials available under the Tutorials feature on the left-hand side of the navigation bar. As in previous articles, we use clinical cases to illustrate PubMed search techniques. Interested readers can work through the examples by completing the actions listed in italic typeface. CASE 1 A 48-year-old woman comes to your office because of increased symptoms of hot flashes. Her last menstruation was 8 months ago, and during the past 4 weeks she has noticed increasingly frequent hot flashes that are particularly bothersome at night. The patient states that she does not want to use any prescription medication but will take a natural product. The patient tells you that she has a friend who uses black cohosh to decrease hot flashes and asks you whether there is evidence that black cohosh decreases their frequency. To answer this question, you search the medical literature for information on the efficacy and adverse effects of this herbal complementary and alternative medicine (CAM) product. PUBMED HOMEPAGE Logon to PubMed (www.pubmed.gov). Hyperlinks to all the NCBI databases are listed across the black header bar beneath the PubMed logo. Tabs below the query box allow you to select different PubMed features. Type black cohosh AND hot flash in the query box and select Go. PubMed will display the results of the search and limit the search to review articles, accessible through a tab feature (Figure 1). The results can be further limited by selecting options available in the updated Limits feature under the Limits tab. From the Division of Primary Care Internal Medicine, College of Medicine, Mayo Clinic, Rochester, Minn. A question-and-answer section appears at the end of this article. Address reprint requests and correspondence to Denise M. Dupras, MD, PhD, Division of Primary Care Internal Medicine, College of Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905 (e-mail: dupras.denise@mayo.edu). 2007 Mayo Foundation for Medical Education and Research LIMITS Select the Limits tab under the query box. Enhanced features of Limits allow for text entry to limit the search to single or multiple author and journal names, free full-text articles, and easier selection of date ranges. More than 1 item can be selected under the language, journal subset, type of article, and age fields. 480
FIGURE 1. The updated PubMed format displays the Features bar as file tabs. A default Review limit is applied to all searches of PubMed. Select English under the Languages and Randomized Controlled Trial under Type of Article, then select Go at the bottom of the page. You have now identified the articles indexed in PubMed that report the results of randomized controlled trials of black cohosh in the treatment of hot flashes. The patient asks what other complementary medicines can effectively treat this symptom. SPECIAL QUERIES PubMed recently introduced the Special Queries feature to help busy clinicians find relevant information quickly. Special Queries is a directory of topic-specific PubMed search strategies for clinicians and health services researchers. Selecting a particular subject, in this case complementary medicine, will limit the search to a subset of articles on this topic indexed in PubMed. Hyperlinks available here allow the user to limit searches by topic or journal subset and link to additional search interfaces. On the PubMed homepage, go to the blue sidebar on the left-hand side of the page under PubMed Services and select Special Queries. Scroll down to Complementary Medicine under Subjects and select it. Notice that the checkbox on the Limits tab is now checked with the Complementary Medicine limit. Type hot flash in the query box and select Go. Further limit the search to Randomized Controlled Trial under Limits. You have now identified other potentially beneficial CAM treatments for hot flashes that have been evaluated in randomized controlled clinical trials. In this case, the use of the CAM Special Query allows the clinician to explore other potential treatment options that may be useful for patients interested in alternative therapies. CASE 2 A 24-year-old woman comes to your office to discuss her concerns about becoming pregnant. She was married 6 months ago, and the couple has now decided they would like to conceive a child. She has not yet stopped taking oral contraceptives. Her sister has neurofibromatosis, and the patient is concerned about the risks for her child. She has not been tested for the genetic disease. Your clinical question is, In patients with a family history of neurofibromatosis, what genetic testing is recommended before conception? CLINICAL QUERIES One way to answer this question is to go to the PubMed homepage and enter terms into the query box. However, PubMed has a new feature, Medical Genetics Searches, that was developed in conjunction with the staff of Gene 481
Reviews: Genetic Disease Online Reviews. This search tool offers built-in filters that can be used to select the most appropriate categories of articles. Go to the PubMed homepage and select Clinical Queries under PubMed Services. Scroll down to Medical Genetics Searches and type neurofibromatosis AND family history in the query box. Select the category Genetic Counseling and click Go. You have now identified potentially relevant articles for the appropriate counseling of patients presenting with concerns relating to the heritability of neurofibromatosis. CASE 3 You have been asked to teach an update on the drug treatment of asthma to a group of nurse practitioners 4 times a year. You want to ensure that you have reviewed all the recent randomized controlled trials on this topic before each session. You decide that the best way to find this information is to search PubMed using Clinical Queries and apply limits to the results. Go to the PubMed homepage and select Clinical Queries under PubMed Services. Scroll down to Search by Clinical Study Category and type asthma AND drugs in the query box. Select the radio button in front of Therapy. Select narrow, specific search and click Go. Select the Limits tab and under Type of Article select Randomized Controlled Trial. Also select Humans and English. Select Go at the bottom of the page. How can you save this information so that you can reexecute the search before future lectures? The next section describes the use of an enhanced tool that makes this possible. MY NCBI Saving Searches. Previous articles in this series described the Cubby feature of PubMed, which allows users to save searches so that they could be reexecuted. This feature has now been greatly enhanced and is currently called My NCBI. This feature is free to anyone who registers. In addition to saving searches, My NCBI allows you to automatically reexecute saved searches at regular intervals and have the results e-mailed to you. It also allows you to set up to 5 filters for PubMed to prefilter any search when the user is signed on to My NCBI. Additional features of My NCBI include the ability to highlight search terms and set additional preferences, including LinkOut and article delivery. Once you have set up your account, this feature makes saving the search described in the previous section easy and ensures that you have the most up-to-date information for each of your future lectures. To use My NCBI, your Web browser must be set up to allow cookies and popups from NCBI Web pages. To set up an account, select My NCBI in the upper righthand corner of the Web browser and follow the instructions. If this feature is not working, hold down the Ctrl (control) key on your keyboard to allow pop-ups or disable your pop-up blocker. Keep in mind that this is a government site and your information is protected. Your e-mail address is requested for the sole purpose of regularly e- mailing you the results of the saved searches if desired and on the schedule that you select. You will know if you are logged on to My NCBI because the upper right-hand side of the screen will say Welcome [your username]. Go to the History tab and select your most recent search by hyperlinking on the right-hand side of the screen. Select Save Search next to the query box. If you are logged on to My NCBI, a window will open that shows you the search strategy and asks if you want to receive e-mail updates of new search results. If you select yes for the option to have updates e-mailed to you, the pop-up window will offer you choices for the frequency of receiving updates. Select OK. View your saved search by selecting My NCBI on the right-hand side of the screen and select the Searches tab. You can modify the settings of the e-mailed searches by selecting the hyperlink at the right-hand side of the screen under Details. Saving Collections. While Cubby allowed saved searches, My NCBI goes one step further by allowing the user to save specific articles in Collections. An individual user is limited to 100 collections and a maximum of 1500 items in each collection. Saving search results in Collections is a 2-step process. To make or save a collection, the user must be logged on to My NCBI. Go to History and select your most recent search. Select an article by checking the box in front of the citation. Save the desired citation to the Clipboard by going to the Send To drop-down menu and select Clipboard. Notice that a colored box appears below the Features tab that indicates the number of articles added to the Clipboard. Also notice that an asterisk appears next to the Clipboard tab, which tells you that items are saved there. Go to the Clipboard tab and select My NCBI Collections under the Send To drop-down menu (Figure 2). As noted previously in the Saving Searches section of this article, if this feature is not working, hold down the Ctrl key on your keyboard to allow pop-ups or disable your pop-up blocker. 482
FIGURE 2. The upper right-hand side of the screen indicates that you are signed on to My NCBI. Once 1 or more articles are sent to the Clipboard, an asterisk appears on the Clipboard tab. Selecting the tab shows the selected articles. If you move a single article to the Clipboard, the list of related articles is exploded to show the titles. If you select multiple articles to be moved to the Clipboard, a Related Links hyperlink will appear next to each article, but there will not be an automatic listing of related article titles. You may also save the article to a My NCBI Collection, which is a new feature of PubMed. At this point, you have the options of making a new collection or adding to an existing collection and deleting the items on the Clipboard. To display your collections, you must click My NCBI and then the Collections tab. You can also manage your collections by merging or deleting them. OTHER FEATURES Additional features available through PubMed can be accessed under Related Resources located on the left-hand blue navigation bar on the PubMed homepage. One very valuable feature is PubMed Central, a database of 500,000 free full-text articles from 200 journals. This material can be accessed by selecting PubMed Central under Related Resources. NLM Mobile provides resources for handheld devices such as Palm and Pocket PC devices. The NLM Gateway feature provides access to many additional resources that are useful to practicing clinicians. The information is categorized into 3 types of resources: bibliographic, consumer, and other information. A database for household products and access to full-text biomedical books are available here. Consumer Health links to MedlinePlus, which is sponsored by the NLM and the National Institutes of Health, provides a wealth of information. Patient information and printable handouts on various searchable disease topics are provided in English and Spanish. This site also includes tutorials, videos of surgical procedures, and information on medications. ClinicalTrials.gov provides a searchable index of all ongoing registered clinical trials. SUMMARY PubMed is an invaluable resource for health care professionals who are looking for primary literature that will keep them up-to-date and provide evidence for making clinical decisions. This resource is continually updated and improved. The New/Noteworthy option on the lefthand blue navigation bar keeps users abreast of new features and developments. Additional guidance is readily available from the Help feature on the left-hand navigation bar. REFERENCES 1. Ebbert JO, Dupras DM, Erwin PJ. Searching the medical literature using PubMed: a tutorial. Mayo Clin Proc. 2003;78:87-91. 2. Sood A, Erwin PJ, Ebbert JO. Using advanced search tools on PubMed for citation retrieval. Mayo Clin Proc. 2004;79:1295-1300. 483
Questions About Using PubMed 1. Which one of the following is the search engine that retrieves citations from PubMed? a. Entrez b. Google c. NCBI d. MEDLINE e. NLM 2. Which one of the following resources provides relevant and reliable patient and consumer health information? a. NLM Mobile b. Related Links c. ClinicalTrials.gov d. Bookshelf e. MedlinePlus 3. Before being saved to My NCBI Collections, citations must be placed on which one of the following? a. My NCBI Saved Searches c. Clipboard d. Nowhere they can be saved directly from the search e. Query box 4. Which one of the following PubMed services allows you to save searches indefinitely? a. Clipboard c. LinkOut d. My NCBI Collections e. My NCBI Searches 5. Which one of the following PubMed services allows you to save individual citations indefinitely? a. Clipboard c. LinkOut d. My NCBI Collections e. My NCBI Searches Correct answers: 1. a, 2. e, 3. c, 4. e, 5. d 484