Guide to Using PubMed

Database Coverage

PubMed provides access to bibliographic information, which is drawn primarily from MEDLINE. PubMed also provides access and links to the integrated molecular biology databases included in NCBI's Entrez retrieval system. These databases contain DNA and protein sequences, 3-D protein structure data, population study data sets, and assemblies of complete genomes in an integrated system.

What is MEDLINE?

MEDLINE is the National Library of Medicine's premier bibliographic database covering medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. MEDLINE contains over 11 million bibliographic citations and author's abstracts from more than 4,000 biomedical journals dating back to the mid-1960's.

In Process Citations

PubMed's in-process records provide basic citation information and abstracts before the citations are indexed with NLM's MeSH Terms and added to MEDLINE. New in process records are added to PubMed daily and display with the tag [MEDLINE record in process]. After indexing data are added, the completed citations are added weekly to PubMed.

Subject Searching

Example: What effect does physical therapy or exercise have on Parkinson's Disease? What are the main concepts in this question?

Parkinson's Disease Physical Therapy Exercise

What happens if you type all of these concepts into PubMed without any other words? PubMed returns a list of citations containing all three of the topics.

Details

How and what is the system really searching?

The statement in the User Query box is how the system translated "Parkinson's Disease Exercise Physical Therapy." The tag [MeSH Terms] refers to NLM's Medical Subject Headings, a controlled vocabulary of biomedical terms used to describe the subject of each journal article in MEDLINE. The parentheses around the parts of the search determine the search order.

The system is going to look for:

1. All articles with the either the MeSH term Parkinson disease or the text word phase.
2. All the articles with either the MeSH term exercise or the text word.
3. All the articles with either and the MeSH term physical therapy or the text word phrase.

Finally, it will combine the results to find articles with all of these concepts.

Searching by Author, Journal or Article Title

To find an article using the author name, in the search box enter the name as follows: lastname initial[au]

To search for articles from a specific journal, the easiest method is to use the Journal Browser function. From the side bar, select Journal Browser from under the PubMed Services section. Enter the journal name, MEDLINE abbreviation or ISSN. You may also enter a single word from the journal title or several adjacent words in the title.

To search for a specific article using the title, select the most distinctive words from the title and in the search box enter as follows: titleword[ti] AND titleword[ti] AND titleword[ti]

Using Limits Function

Using the limits button will allow you to narrow your search using any of the following criteria:

• Fields - terms in only a specific field, e.g. Text Word, Title Word, MeSH Terms
• Publication Types - e.g. Clinical Trials, Review Articles
• Only items with abstracts, place a check in the box
• Languages
• Subsets - e.g. Nursing, Dental
• Ages - by specific ages groups, e.g. children, aged
• Human or Animal or Both
• Gender
• Entrez Date - Date added to the database
• Publication Date

Using the MeSH Browser

The MeSH Browser function is located in the sidebar under PubMed Services. You can use it to find where a MeSH Term falls in the Subject Tree.

The above picture illustrates the entry for Parkinsonian Disorders. It defines its use of the term and shows where the term is located in the MeSH Tree. You may then choose one of the more specific MeSH Terms, e.g. Parkinson Disease, and click on it. You will then jump to the display of Parkinson Disease in the MeSH Browser.

You may then choose to limit to certain subheadings, e.g. drug therapy or therapy. If you choose more than one, they are searched using an OR.

Click in the check boxes here to Restrict Search to Major Topic headings only and/or to Not Explode this term (i.e., do not include MeSH terms found below this term in the MeSH tree).

After you click all of the appropriate check boxes, click on the Add button to have the MeSH Term added to your search statement. You may then choose to add other MeSH Term as detailed above and add them with either an AND, an OR, or a NOT operator.

Once you have finished compiling your search statement, click on the PubMed Search button to run your search.

History

Lists your recent searches up to 100. After 1 hour of inactivity, the system times out and the list disappears. To combine searches, use the # before search number, e.g. #5 AND #6.

Clipboard

You may use the Clipboard to save up to 500 citations. After 1 hour of inactivity the list disappears. To use this feature, check the box next to the items you wish to place in the Clipboard.

Once you have made your selections, click on the Add to Clipboard button. To retrieve your list, click on Clipboard under the search box:

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While in the Clipboard you may then choose to Sort the citations by Author, Journal title or Publication Date. Displaying Your Search Results PubMed has several different display formats. The default display is Summary, which displays the basic citation information as show in the above illustration. Other display options that will be useful are:

Abstract

Displays full citation information, including author affiliation, the text of the abstract when available, and the publication types associated with the article.

Citation

Displays all of the fields in the Abstract display plus the MeSH Terms used to index the article.

MEDLINE

Displays the citations in the two letter tagged format which is needed to import citations into EndNote and other Bibliographic Managers.

To change the display from one format to another, select the desired format from the pull down menu.

Then click on the Display button to reformat the page into the selected Display format.

Downloading and Saving to a Disk

To Save your entire set of search results:

1. Select and reformat the results in the appropriate Display format;
2. Click the Save button;
3. When the Save Downloaded File dialog box opens, change the name of the file using the following convention: filename.txt

To Save select items, you may:

1. Use the Clipboard function and save as noted above from the Clipboard screen; or
2. check the boxes next to the desired citations, and then follow steps 1-3 from above.

Sending Results via Email

To send results via email, follow the above steps to first save your results as document on your computer or disk. Create an email message with the file of saved results as an attachment.

Printing

After selecting and displaying the results in your desired format, click on the Text button. Once the information displays on the screen, you may print using your Web Browser print functions.