An Introduction to PubMed

http://www.ncbi.nlm.nih.gov/PubMed/

Additional PubMed help is available at
http://www.ncbi.nlm.nih.gov:80/entrez/query/static/help/pmhelp.html

What is PubMed?

PubMed is the National Library of Medicine s search service that provides access to:

MEDLINE: an international bibliographic database of over 4000 biomedical journals from 1966-present.

PreMEDLINE: new records are added daily; will appear with the tag [MEDLINE record in progress].

HealthSTAR: a health administration and technology/research database; also includes full text of practice guidelines.

PubMed also provides links to molecular biology databases of DNA sequences, population data, and genomes.


Subject Searching
PubMed may be searched by entering keywords or phrases into the text box. You may enter one or more terms and press the enter key or click Go. PubMed will search multiple words as a phrase if it recognizes the terms. Otherwise, PubMed will search the words separately and combine with AND. PubMed will also automatically try to map your term to a MeSH heading.

Example: vitamin c common cold is searched as vitamin c AND common cold

PubMed does not perform adjacency searching; instead it uses a Phrase List against which to match terms. Enclosing a term in quotation marks forces PubMed to check a second Phrase List. If the term is still not found, the words are combined with AND.

Example: "pressure point "

When using keyword searching, you may sometimes want to truncate (*) words to allow for variant word endings.

Example: bacteri* retrieves bacteria, bacterium, bacterial, etc.

 

Medical Subject Headings (MeSH)
Using MeSH can help you achieve specificity in results and may be the most precise way to do Subject searches. Articles are entered into MEDLINE using the Medical Subject Headings, NLM's controlled vocabulary for indexing articles. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts.

Index
One way to identify and select MeSH terms for a search is to use the Index feature found on the function bar below the text box. Click Index, pull down the All Fields menu, select MeSH Terms, and enter the term in the View Index text box. Click View. To select more than one term, hold down the Control key and click on each of the terms you wish to include and click on OR to place all terms in the text box. MeSH Subheadings, which restrict a term to a specific aspect, may also be selected here.

Example: asthma/chemically induced

HINT: Subheadings are useful common categories such as diagnosis, drug therapy, etiology, prevention and control, surgery, which can help to limit your search. The use of subheadings might sometimes eliminate some useful articles.


MeSH Browser

Another way to select MeSH terms is to use the MeSH Browser link, found on the blue sidebar, which allows you to browse for appropriate terms. Enter the term in the text box and click GO.

Scroll down the page to see everywhere the term appears in the MeSH "Trees", a hierarchial subject category display of Mesh terms. For example, if you browse this list for diabetes, you can select from a host of terms including diabetes mellitus, obesity in diabetes, diabetes mellitus insulin dependent, or diabetes insipidus.

To further refine your search click on Detailed Display:

MeSH Subheadings, which restrict a term to a specific aspect, may be selected here.

Check Restrict Search to Major Topic headings only to focus your search to those documents in which your term is considered the major point of the article.

Check Do Not Explode this term to not include MeSH terms found below your term in the MeSH tree.

All Fields

If you know the Medical Subject Heading you may enter it directly into the text box. Click on Limits, pull down the All Fields menu and select MeSH Terms or MeSH Major Topic.

HINT: Limiting to MeSH may eliminate PreMEDLINE citations because these articles have not yet been indexed.


Limiting a Search
Limits allow you to search specific fields using pull-down menus for Publication Type, Language, Subsets, Ages, Human/Animal, Gender, and Date. Click on the word Limits below the text box.

You can click on Limits at any point in your search to apply, drop, or change the limits. A check mark in the box next to the Limits indicates that limits are active for the search.

HINT: Unless changed or unless the check mark is turned off, limits remain active for an hour. If you start a new search, make sure to refresh the limits!


Combining Concepts: The Search History
Continue to add terms to your search until you have entered all the concepts (clear the text box before entering a new concept). Or you may enter the concepts separated by search operators as illustrated below.

The History function keeps track of your searches and numbers them, allowing you to go back to earlier searches and combine or modify them. The History button is found on the function bar under the text box.

HINT: You must use the # symbol before the search numbers and search operators (AND, OR, NOT) must be capitalized.

AND Articles containing all of the terms you selected. AND narrows your retrieval

OR Articles containing one or any of the terms you selected. OR broadens your retrieval.

NOT Use NOT to eliminate terms or sets you do not wish to appear in your search.



Title Word Search
Limiting a search to a word found in the title is often a good way to reduce large search results. You can do this by entering the term in the text box. Then click on Limits, pull down the All Fields menu, and select Title Word. You may also limit to title by entering the term followed by [ti].

Example: non-Hodgkins lymphoma [ti]


Author Search
To retrieve articles by author, enter the author's name in the format of last name followed by initials. Although initials are optional, search retrieval may be quite large (and inaccurate) without them, especially for common last names. Click on Limits, pull down the All Fields menu, and select Author Name. Or follow the name with [au] as shown below. The Index provides a list of author names and variations.

Example:


Related Articles Feature
A helpful PubMed feature is the ability to find documents that are similar to a document which you find of interest. To retrieve related articles for a given record, click on Related Articles, which appears at the right of each citation.

The Related Articles will display in relevancy rank order, becoming less relevant the further down you progress in the display. Limits are disregarded by the Related Articles function. For example, foreign language articles will appear even if your original search was limited to English only.

The Related Articles feature is a good way to discover synonymous/related concepts that you may not have considered in your original strategy. Examine the MeSH terms (use the Citation display) to look for alternative or additional MeSH terms to use in a modified search.


Clinical Queries
The Clinical Queries search mode is designed with clinicians in mind. It works only for diagnosis, etiology, therapy and prognosis questions. Built-in search "filters", tested by the EBM Working Group at McMaster University, screen for clinical relevancy.

The "Table for Clinical Queries Using Research Methodology Filters" outlines the filters used for each of these four categories. The objective of Clinical Queries is to reduce retrieval to articles that report research conducted using specific methodologies.

For example, a therapy search will retrieve randomized controlled trials and a diagnosis search will retrieve studies which employed sensitivity and specificity criteria. If you wish to retrieve everything on a subject, you should not use this search mode.


Citation Matcher
The Citation Matcher feature allows you to find/verify citations using bibliographic information such as journal name, volume, issue, page number, publication year, or author. This feature is especially helpful when you have incomplete bibliographic information.

If you enter only the Journal Name, you will get a "Table of Contents" type listing starting with the most recent issue of the journal. This can serve as a current awareness service.

Displaying Search Results
PubMed displays search results in batches; the default is 20 records per page. To change the default, the Show pull-down menu allows you to increase the number of records displayed on a single page up to 500. This is convenient when you wish to browse the entire display to choose selected articles to save or print.
PubMed citations initially display in Summary (Author, Title, Journal, PubMed ID) format. Documents can be viewed in other formats including Brief (author, PubMed ID), Abstract (Author, Title, Journal, PubMed ID, Abstract), Citation (Author, Title, Journal, PubMed ID, Abstract, MeSH Headings), and MEDLINE (for importing into citation software - Author, Title, Journal, PubMed ID, Abstract, MeSH Headings).

Individual citation
Display by clicking on the author s name. This causes PubMed to display the Abstract format.
All Citations
Select a display format and then click Display to view a different display for all citations on a page.
Selected Citations
Click on the boxes to the left of each author name to select specific citations, then select a format from the Display menu and click Display.


Printing Search Results
Once search results have been Displayed in the desired format (Summary, Brief, Abstract, Citation, or MEDLINE), click on the Print icon on your browser to print the results.

Saving Results to disk
Results may be saved to a disk or hard drive. Once search results have been Displayed in the desired format (Summary, Brief, Abstract, Citation, or MEDLINE), click on the Save button next to the Display pull down menu.
A "Save As" Dialog Box will appear. Title the name of your search in the File Name Box. Click Save. These files can be opened in Word, WordPerfect, or Notepad.

Saving to Citation Software (Reference Manager, Endnote)
To import results into Citation Software, you must display your results in MEDLINE format. Click on the Save button next to the Display pull down menu. Title the name of your search in the File Name Box. Click Save.


Saving Search Strategies
Search strategies may be saved in PubMed. This is useful for re-running searches on a periodic basis to keep up-to-date on topics of interest to you.
Create your search strategy and limit your strategy as desired. When this is complete click on the Details button. This will display a "behind the scene" look at exactly how your search strategy was executed. Click on URL under the PubMed Query Details Box. This will transform your search strategy into a URL address. Click on Bookmarks on your Web browser and select Add Bookmark. This will book mark a web address called Entrez-PubMed. Whenever you want to perform a search on the selected medical topic, simply click on the Bookmark.
You may want to edit the name of Entrez-PubMed to something meaningful. To do this, Click on Bookmarks and select Edit Bookmarks. A bookmarks Edit Window should appear. Click on Entrez-PubMed from the list that appears. Next, under Edit click on BookMark Properties. In the name text box, change Entrez-PubMed to a meaningful name for your search. (Do not save strategies created using Search History search numbers.)

Limiting your strategy to the Last 30, 60 or 90 days. It is possible to limit saved search strategies to search only the last 30, 60 or 90 days of literature that has been entered. To do this, click on Limits. On the limits page, select either 30 Days, 60 days, 90 days, 180 days from the Entrez Date pull down menu.

ClipBoard
The Clipboard allows you to group selected citations from one or more searches. You may then print or save the citations. A maximum of 500 citations can be placed in the Clipboard. Clipboard items will be lost after one hour of inactivity.
To add items to the clipboard, click on the check box to the left of the citation and then click Add to Clipboard. Once a citation has been added to the Clipboard, the record number color will change to green.

Once you have added items to the Clipboard, you can click on Clipboard from the Features bar to view your selections. In the Clipboard, you can sort citations by author, journal, or publication. Click on the Clipboard Sort pull-down menu to select a sort field. Next click on Display.

Link Outs
PubMed is gradually adding links to various publisher sites where users may immediately access the full text of selected citations. Most online journals require a subscription. UIC subscribes to numerous online journals which may be accessed through PubMed's LinkOuts.

Once your search is complete, click on LinkOut in the Display pull down menu. This will show a brief display of the articles and available link outs. LinkOuts for Karger, Ideal, MDConsult, Blackwell Science, or Elsevier will let UIC users link directly to the article._ Click on the linkout icon that appears in the search display to access the article.

In order to link to these online journals you must be dialing in through UIC, using a UIC ethernet connection, or have the Bluestem proxy set on your computer.

Special Instructions for MDConsult and Science Direct articles:
In order to access MDConsult articles, you must set up a personal edition through UIC at http://home.mdconsult.com/groups/uic.html. There is no charge for this special feature When you click on MDConsult in PubMed, you will be prompted for a user name and password. Use your MDConsult personal edition account information.
In order to access Science Direct articles - you must first click on Elsevier and then click on Science Direct.

Please note:

 

 

 

J. Dorsch / S. DeGroote 07/00