Introduction to PubMed

PubMed was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH). It functions as an interface to allow MEDLINE to be searched by the ENTREZ search engine. It also provides links to other relevant citations, full-text articles at journal Web sites, the other NCBI databases (such as Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, OMIM, and many others) and other related molecular biology databases and tools. This feature is referred to as Linkout.

MEDLINE is the NLM's premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences.? MEDLINE contains bibliographic citations and author abstracts from more than 4,800 biomedical journals published in the United States and 70 other countries. The database contains over 16 million citations dating back to the 1950's. Coverage is worldwide, but most records are from English-language sources or have English abstracts. 

Publishers participating in PubMed electronically submit their citations to NCBI prior to or at the time of publication. If the publisher has a web site that offers full-text of its journals, PubMed provides links to that site as well as biological resources, consumer health information, research tools, and more. There may be a charge to access the text or information, but often journal articles older than 6 months can be accessed free.

PubMed Central is a newer sub-section of PubMed which archives only free full-text journal articles. This is particularly convenient because references can be downloaded immediately.

When the PubMed page comes up, select the "Preview/Index" tab. 
Then scroll down to the search box flanked by "Preview" and the "Index" buttons on the right.
To the left is a pull-down menu labeled "Fields". This menu shows all the fields which are present for each record in the PubMed data base.

It is possible to make a search considerably more efficient by limiting it to only certain fields. If for example you have a key term, but also the name of an author (or authors), a short list of publications can be produced by searching for the name limited to the author field. This search will return the intersection of the search terms.

Type "Sickle Cell Anemia" into the search box. Click on the "Index" button.

A long list of index terms will appear which contain "sickle cell anemia". Hold down the "control" key while clicking on index terms of interest. How does this produce a different result from simply clicking on a term or holding down the "shift" key while clicking?

Then click on the "OR" button. A new search will appear in the search box at the top of the page. Click on the "Preview" button to see how many hits are returned by this query.

The results of the "Preview" show us that there are 31 hits. Note that the Entrez search engine will search "All Fields" for the union of these three terms.

In order to further reduce the number of hits, click on the "Limits" tab. This should bring up a screen as shown in the thumbnail to the left.

• Select "Links to Free Text". This will limit the search to only those journal articles for which the full text is available on-line at no charge.

• Select "5 years" from the "Dates" menu.

• Select "English" from the "Languages" menu. 

• Select "Review" from the "Type of Article" menu. This will limit the search to review articles only, eliminating research papers, clinical reports, letters, editorials, etc.

Click on the "Preview" tab to see the results. As of Feb. 3, 2006, there are no hits which match this search. Notice that the search now shows not only the boolean query, but the limits which were placed on it.

Since the search was too stringent, return to the previous search, and click on the ""31" link. Go to the "Sort by" pull-down menu, and sort by "Publication Date".

Select references of potential interest, by clicking in the check boxes (shown by the small black-and-white arrows). Go to the "Send to" pull-down menu (shown by the large red arrow), and select "Clipboard". 

This action places only those references you have selected on anther screen called the "Clipboard". Notice that after you do this, the references which are on the clipboard are now indicated with green numbers!

Click on the "Clipboard" tab. Go to the "Display" pull-down menu, and select "Abstract" as shown in the image to the left. 

Review the abstracts to determine which you believe will be useful for your poster.

Now, return to the "Display" pull-down menu, and select "Summary" again. Click on the check boxes of the references which you believe will not be useful for your poster. Go to the "Send to" pull-down menu and select "Clip Remove".

The list of references can be improved and enlarged by selecting the most relevant hits, and then clicking on the link to "Related Articles" (red text).

Any additional references can be added to the clipboard by clicking on the checkboxes, and then sending them to the clipboard.

Send your list of references to a text file. Print the file and hand it in to your Instructor!