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PubMed: Getting Better Results

www.library.uthscsa.edu Accessing PubMed


Although PubMed is freely available, access to full-text through PubMed is limited. Logging in through the Librarys web site provides access to electronic journals subscribed to by the UT Health Science Center Libraries. See pages 9 and 10 for additional assistance accessing full-text.
A quicklink to PubMed is available in the Databases menu. This special link can also be bookmarked.

Basic Search
The first screen in PubMed provides access to the basic search function. Type any combination of terms, authors, etc. in the search box. If you choose to combine terms, you can use Boolean operators such as AND/OR/NOT. Remember they must be capitalized.

As you type in the search box you will notice the Term Suggest feature. The drop down list supplies suggested terms as you type. You can also select a search from the list by clicking on it. Please note this list of suggested searches is based on frequent PubMed searches and may not help your search strategy. Consider the suggestions to be spelling rather than searching help.

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The Basic Search and Automatic Term Mapping (ATM)


PubMed takes the words typed into the search box and through a process called Automatic Term Mapping (ATM) translates them into MeSH (Medical Subject Heading) terms, which reflect concepts from the complete article and are assigned by an indexer who has read the article. It also searches for the same words as text words (words appearing in article titles and abstracts). If PubMed detects what it interprets as a journal or author name, it searches for those too. PubMed usually does a good job interpreting your search. In some cases you will get better results by using MeSH and Advanced Search features described in the following sections. For a basic search enter your search terms and click Search. In this example, we are looking for information about vitamin c and the common cold. For the basic search we typed in vitamin c common cold. Note: To search for an exact phrase use quotation marks around the phrase.

On the right hand side of the results page, Search Details shows how PubMed translated your request. Click See more to see complete search.

Using the MeSH Database


While keyword searching is ok, using PubMeds MeSH Database is one way to improve your searches. The MeSH Database allows you to explore available MeSH terms, instead of having PubMed select a term for you. When using the MeSH Database, you can also View the hierarchical MeSH trees to see broader and narrower terms related to the one you have selected
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Decide whether or not to include these broader and narrower terms in your search Restrict your term to the major focus of the article(s) Choose subheadings, such as diagnosis, drug therapy, complications, etc., which will further refine your search.

MeSH terms reflect ideas and concepts from the entire article, not just those in the title and abstract. To use the MeSH Database, select MeSH from the drop down menu above the search box. The page will not change, but you can still use the search box. Enter a single term, such as cold and click Search. Results will be a list of terms and their definitions (scope notes) from the MeSH Database.

In the example below, we can see that Common Cold is the best MeSH term for our search. Click on the term for more information and options.

The scope note is repeated on this page. Beneath the scope note, the range of subheadings for this term appears. Subheadings are used with headings and can be useful in focusing your search. However, if there isnt a subheading for your topic, dont choose any more MeSH terms which help limit your search can be added later.

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Typing any of these entry terms will cause PubMed to automatically look for articles indexed to common cold

For our search well select Common Cold. Quick Tips:

Broad Search PubMed automatically includes narrower and more specific (indented) terms in your search. This is usually called exploding a term. When in doubt, explode! You will be able to limit your results as you continue searching by adding more terms.
Narrow Search If you do not want to include the narrower terms, check Do not include MeSH terms found below this term in the MeSH hierarchy above the tree (immediately below Restrict Search to Major Topic Headings only). Narrower Search Click in the box Restrict to MeSH Major Topic if you want the term to be the main theme or focus of the article, articles that talk about the topic in a more minor way will not be included. After making your choices, select Add to search builder button with AND or OR from the right column menu. You can then look for more terms to add to your search in MeSH or you can immediately search PubMed but pressing the Search PubMed button. When you are satisfied with your search term click Search PubMed.

To create a search from a MeSH term, click Add to search builder. Then click Search PubMed to begin search and view article results.
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Advanced Search
Beyond the Basic Search features, Advanced Search options provide ways for you to refine your search. The following section will discuss advanced features every PubMed user should be familiar with. To access Advanced Search options click on the Advanced Search link located just above the basic search box. At any point you can click on Advanced Search to refine or modify your search. The Advanced Search screen also shows your search history.

The Advanced Search page is divided into sections that will help you refine your search.

Search History
When performing an in-depth search we suggest breaking your search topic into manageable pieces and searching for each term one at a time. You can then use the Search History section to combine your terms. This allows you to quickly and easily edit or modify your search by adding or subtracting terms. Search History also allows you to return to results from a previous search. Your search history should be saved for up to eight hours if you do not close your browser or clear your browser cache.

Clicking on the number allows you to combine terms using AND/OR then execute a search.

Click on the number under the Results column to return the results from that search.

Search using Single Citation Matcher


Occasionally you may have a specific citation you want to search for in PubMed, you may want to search by a specific author or journal, or you may want to narrow results by a specific publication date. The best way to execute this type of search is by utilizing the Single Citation Matcher section. Single Citation Matcher helps you locate an article by filling in the information you have about a citation (e.g., author, title, journal, volume, issue, page) by field. Often fewer details work best in this search.

For the best results, enter information into one or two fields, such as title only, journal and title, or author and title.

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Filtering Results by Topics, Languages, and Journal Groups


You may decide that your search has retrieved too many citations. Or you may want to perform a more precise search. To reduce the number of citations or get to results that better match your criteria you can apply filters using the options that appear on the left column of the search results pages. Filter options include: languages, human/animal research, participant gender and article type which can be used to narrow your search. Note especially the limit for Ages; select age groups instead of using terms like pediatrics or geriatrics, which refer to practice specialties. These options can be toggled on and off by clicking your choice.
We recommend not using the Text availability filters because you have access to many more journals when using PubMed through the Librarys website and clicking the HSC Link button. See Page 9.

Use the Choose additional filters option to display additional filtering choices.

Once you have set filters you will notice that the Results page now displays an icon indicating that limits were activate on the search. These limits will remain active if you perform another search. Use the Clear all link in the Filters Activated area to remove filters from your results. Use the filters column to add additional filters.

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Viewing and Managing Results


Results initially appear in the Summary format. To view greater detail, including the abstract, click on the title of the article (underlined in blue).

Review limits. Press Clear or select different choices to alter results.

Free full-text articles from PubMed Central are freely available to everyone.

The format of the results list can be changed by clicking on Display Settings at the top of the results list. You can change the default format (Summary, Abstract, etc), the number of results on each page or you can sort the results from Display Settings.

Alternately, as you scan citations, place a mark in the checkbox next to those for which you wish to see detailed information. After going through the set, change the Display Settings. Only your selected citations will be shown.

Retrieving References and Full-Text


To access the full text of an article the best option is to view the citation in the Abstract format. To do this either modify the Display Settings or simply click on the title from the main results page. In Abstract format you will be able to read the abstract if available. In this view you will also see additional options in the column on the right. Features include the ability to find full text and find related articles.
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To find articles that are similar in scope to the article currently showing in Abstract format see the Related Articles box. Here you will find additional articles that are similar based on the MeSH terms used in the article you are viewing.
Use HSC Link button for full text access. Only use publisher buttons that are labeled FREE.

Related Articles are shown here

The best way to access the full text of an article is through the HSC Link button which is available in the Abstract view when you have accessed PubMed through the Librarys website. To the right of the article you will see the button, some citations may also have a publishers button which is supplied by PubMed. The UT Health Science Center at San Antonio Libraries have access to many journals that do not have the publishers button. Therefore, it is best to click to see if the Library has a subscription to the e-journal. If we do, the article will usually appear after several moments or a link to the article will appear. If the Library does not provide electronic access you can use the HSC Link button to check library print holdings or to order the article through Interlibrary Loan - ILLiad service.

Additional Options
Print, Saving, and E-mailing PubMed Citations
If you find the full text of an article through PubMed, remember to print, save, or e-mail the file while you are looking at it. When printing, saving, or e-mailing from PubMed, only citations are included not PDF files. Click the checkbox in front of the citations you wish to print, save, or email. Use the Send to menu to select, File (for saving or printing), or E-mail to send yourself a message. To export to RefWorks or EndNote, select the Citation Manager. (PubMed will then create a file type nbib that can be imported into RefWorks or EndNote.) You can choose type of format for your file (Summary, Abstract, MEDLINE, etc.) before saving.

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Using the Clipboard to Manage References


Additionally you can use the Clipboard as a holding area where you can save references from multiples searches to be printed/saved/e-mailed later. Think about the Clipboard as a shopping cart feature. Select the citations to save to the Clipboard by clicking the checkbox for each, then select Clipboard from the Send to menu. You can do more searches and continue adding citations to the Clipboard. Articles already saved to the Clipboard that appear in later searches will include the phrase Item in clipboard in green, alerting you that you do not need to save the citation again. The Clipboard will also become line #0 in the Search history. Results view:
Click to view items in the clipboard

Text indicating Item already in clipboard

When ready to print, save, or e-mail, click the number of items displayed next to Clipboard from the box to the right of the results. From within the Clipboard, you can remove a reference, if desired, by clicking the Remove from Clipboard next to each Clipboard item. Once you are satisfied with the collection of references in the Clipboard, you can print, save, or e-mail as before. Items saved to the Clipboard are removed after eight hours of inactivity. Clipboard view:

Remove all Items or a single item with by click on the text

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Additional Resources
The National Library of Medicine produces several tip sheets and tutorials for using PubMed. Additional library resources including tip sheets are available through the librarys website (http://www.library.uthscsa.edu). National Library of Medicine PubMed Help Visit PubMed Help for additional information about using PubMed. Included are links to popular topics as well as Frequently Asked Questions and tutorials.

PubMed Online Training & Tutorials http://www.nlm.nih.gov/bsd/disted/pubmed.html PubMed Basics http://nnlm.gov/training/resources/pmtri.pdf Searching PubMed with MeSH http://nnlm.gov/training/resources/meshtri.pdf

To report problems with PubMed, contact the Library or directly to the National Library of Medicine using the Write to the Help Desk feature.

Library Resources Information Librarians (210) 567-2450 Email askalibrarian@uthscsa.edu

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