Introduction to PubMed
PubMed: Medline as developed by the National Center for Biotechnology Information (NCBI) and National Library of Medicine (NLM)
Access: Access to PubMed is Via our website: www.base-library.nhs.uk/BWH_lib/ or via the National Electronic Library for Health (NELH) at www.nelh.nhs.uk or you can type the URL in the address bar on your Internet search engine: www.ncbi.nlm.nih.gov/entrez/query.fcgi
Getting Started: You will not need a password to access PubMed. Just follow one of the routes described above. The first page looks like this:
PubMed searching is easy. The black menu bar has links to other resources provided by NCBI. We are only interested in PubMed.
Search terms are entered in the query box. The features bar below the query box provides access to additional search options. ______________________________________________________________ 2
Searching – Author search 1. Enter the author’s name in the query box using the format of last name then initials. Do not use any punctuation (eg. Smith A). Click the Go button. PubMed automatically truncates for varying initials and designations like Jr. or Dr.
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______________________________________________________________ Searching – Keyword / Subject 1. Type your keyword or phrase in the query box and click the “go” button or press the return key.
PubMed has an automatic term mapping feature – So it will automatically find the correct MESH subject heading for your term. The results for your search are displayed in the results box, beneath the features toolbar. The first 20 results are listed below that.
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To continue building your search, simply click the “clear” button next to the query box. Now enter your next search term or phrase. Keep building your search sets in this way.
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Each of these search sets is automatically held in your History. The history can then be used to combine sets as described later in this guide. ______________________________________________________________
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Combining search terms You can combine terms using the Boolean operators AND, OR, NOT. If your search includes Boolean operators then they must be entered in capital letters as below.
You can also combine your sets as you build them up. They are located in the History. ______________________________________________________________ Combining sets / using the History. As you build your search your search sets are automatically placed in the History. Each time you put in a new search term or phrase, PubMed places a copy of your last search in the history. When you wish to combine sets: 1. Click the History button on the features bar. The history page opens like so:
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Each search has been given a set number. To combine these sets you need to type the set numbers with the appropriate operator. For Example, to combine sets 1, 2 and 3 using the operator and you would type: #1 AND #2 AND #3 4
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In the query box and press the go button.
When you have finished with the items in the history or you wish to start a new search with no history simply click the Clear History button. This will clear all the items in your history. ______________________________________________________________ Previewing your searches At any point you wish during searching you can preview the number of hits your search will yield by using the preview / Index button on the features bar:
Type in your search terms as normal but then rather than clicking the go button click Preview.
The search will be performed but the results are not added to your history (until you click the Go button). You can build up sets and defer displaying the documents until you have completed your search. Clicking on the Go button will display the set’s results in the usual way.
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Limiting your search 1. Click the Limits Button on the on the features bar. The limits screen will open as below.
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You can now refine your search using the pull down menus. For example if you wanted to limit the search to clinical trials open the Publication type pull down menu and select clinical trial.
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Continue to limit your search using the options available and then click the go button. The limits will be placed on your last search set. Limits stay on once they have been set. Any searches you do after the limits are set will automatically be limited. To switch off the limits click the limits box once, the tick in the box will disappear and the limits are switched off.
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Displaying / Selecting Articles / Clipboard 1. The display format can be changed by using the pull down menus on the documents tool bar:
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To change what is displayed use the summary pull down menu to change what is displayed. Choose from brief, abstract, citation etc.
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To sort the citations into date order, or to sort alphabetically by author or journal title use the sort pull down menu.
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PubMed displays your results in batches. The default for the number in each batch is 20. This can be changed by opening the show pull down menu.
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To select the articles of interest just tick the box next to the article details. At the end of each page click the Send to drop down menu and select Clipboard:
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To send these items to the Clipboard click on the Send to button. You will receive a confirmation message telling you how many items are on your clipboard.
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To view the abstract (if one is available), click the author hyperlink (ie authors names in blue) and the full reference for the article will be displayed or click the abstract icon If the Article is available free of charge in full text form then the full text icon is displayed . Simply click to see the full text.
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To remove articles from the clipboard first go to the clipboard by clicking the Clipboard button on the features bar. Select the items to be removed by putting a tick in the checkbox. Open the Send to pull down menu and select Clip remove.
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Click the send to button and the items are removed from the clipboard with the message below:
______________________________________________________________ Saving / Emailing search results 1. You can save all of the results of your search to disk using the Send to drop down menu and button
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Select File from the drop down menu and click the Send to button. A download will start.
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Click the save button, select your drive, give your file a name and save as normal.
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When the download is saved a Download Complete box will open.
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The send to drop down menu also has Text and Email options. (Clipboard we have covered already, Order is never used) Selecting Text will display all of the citations in the current set in plain text format. Selecting Email gives you the option of sending all the citations in your last search set to any valid email address.
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Select the format you want, the order you want the citations in and add a short message and the email address and click Mail.
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Your email is sent and PubMed displays the set you just sent with a message confirming to whom the email has been sent.
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Additional Features. PubMed Services. The PubMed services menu on the left of the screen (as below) has some useful tools which are explained below.
Journals Database
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The Journals database can be used to find journal titles. Type the name of the Journal, the Medline abbreviation or the ISSN and click go. You can truncate the name using the asterisk (*) wildcard. For example, eng* will find English, England etc.
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MESH Database
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Use the MeSH Database searches for exact MeSH terms. The will give you your exact term or a list of possible matches to choose from.
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Select the MeSH terms you want to search on using the tick boxes as before (when selecting articles).
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Then from the Send to drop down menu chose to send to either (Text, File, Clipboard are there as before) send to: Search box with AND Search box with OR Search box with NOT
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If you chose to Search box with AND this will combine the MeSH terms you’ve selected with the Boolean operator AND. A search box opens showing which MeSH terms are to be searched. If the correct terms are there then click the Search PubMed button.
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The search is carried out as normal.
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Single Citation Matcher / Batch Citation Matcher 1. The Single Citation Matcher can be used to retrieve a full citation for which only a part of the citation is known.
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Type the known details into the appropriate box, click the search button and PubMed will retrieve any matching articles that are indexed.
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The Batch Citation Matcher can be used to retrieve the PubMed IDs for many articles all at the same time.
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You will need to enter the details in the format shown on screen.
______________________________________________________________ Clinical Queries Clinical Queries: Is a specialised search query, with built in research methodology filters designed for clinicians. You choose if you want your search to be broad or narrow (sensitive or specific) and indicate what type of question is being asked (i.e. Therapy, Diagnosis, Prognoisis or Etiology (Causation). The systematic reviews feature is for locating systematic reviews or the medical genetics feature for medical genetics research papers. 1. Click the Clinical Queries. The screen opens like so:
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You can search whichever of the categories you want. Type your search term (or terms using Booloean Operators) in the query box and press the go button. Remember though, overcomplicating your search with too many search terms will yield zero or very poor results. For example. If your question is: “What are the risks to mother and baby if mother contracts chickenpox in pregnancy” don’t type the whole question. Your search strategy should be: chickenpox AND pregnancy
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There are other features on PubMed that have not been covered in this guide. The reason for this is that in the main they are features of no use. You will not need the document ordering features or such like as your librarian should be able to get any documents you need quicker and cheaper than you could buy them through PubMed. For more information on PubMed try the Overview, Help and Tutorial sections.
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