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PubMed: Quick Guide


Use this URL to access the UC-customized version of PubMed, with links to the full text of articles:

http://uclibs.org/PID/17708

Description: PubMed is the primary database for researchers in the fields of biochemistry, molecular biology, and related life sciences. It comprises over 20 million references to articles published in more than 5,200 current biomedical journals from the United States and over 80 foreign countries. It was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM).

PubMed Coverage:
MEDLINE (1966-present)
OLDMEDLINE (1946-1965)
In-process records (new citations not yet fully indexed)
Additional non-MEDLINE citations

For more information: What's the difference between MEDLINE and PubMed?

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Basic Search Techniques

PubMed

Keyword Search

Enter one or more subject terms (e.g. molecular motors) in the search box and click Search. PubMed automatically combines (ANDs) terms together.

Automatic term mapping matches your search terms with MeSH terms (Medical Subject Headings) to improve search results.

Example: A search for heart attack retrieves articles that contain the words heart attack in their titles or abstracts. It also retrieves articles that contain the words myocardial infarction, the medical term for heart attack, in their titles, abstracts, or MeSH terms.

Search Details shows how PubMed has interpreted your search.

To search by keyword from the Advanced Search screen, use the Search Builder and select All Fields from the pulldown menu.

Author Search

Enter the author's last name first, followed by initials, without punctuation (e.g. koshland me). For authors with citations from 2002 and later PubMed also allows searching by last name, full first name and middle initial (e.g. koshland marian e). To search for an author when only the last name is available add the author search field tag [au] (e.g. koshland [au]).

To search by author name from the Advanced Search screen, choose Author from the Search Builder pulldown menu.

Journal Search

To retrieve articles from a specific journal, enter the full journal title (e.g., Current Biology) or use the MEDLINE title abbreviation (e.g., curr biol) in the search box. Qualify single word journal titles using the Journal Title [ta] search field tag. (e.g. Cell [ta]). Note: In the search box, an author's name or journal title can be combined along with subject terms, such as thorner protein kinase or curr biol protein kinase.

If you only know part of the journal title, go to the Journals Database, in the Resources pulldown menu (top left corner of screen, Resources > Literature > Journals in NCBI Databases). Enter the title words and click Go. You can add journal titles from the Journals Database to your PubMed search by using the Send to Search Box feature.

To find a journal title abbreviation, search the NLM Catalog for Journals referenced in the NCBI databases.

Boolean operators (AND, OR, NOT)

Use AND, OR, or NOT to combine terms or phrases. PubMed processes all Boolean connectors in a left-to-right sequence.

Use parentheses to specify the order in which PubMed processes your search terms; to search for articles containing "common cold" and either "vitamin C" or "zinc," enter common cold AND (vitamin C OR zinc). Terms inside a set of parentheses are processed as a unit and then incorporated into the overall strategy.

Truncation (Wildcards)

Use an asterisk (*) to replace zero to many characters at the end of a word. For example, bacter* retrieves bacteria, bacterium, bacteriophage, etc. Truncation turns off automatic term mapping and the automatic explosion of a MeSH term; for this reason, truncation in PubMed is not generally recommended.

Related Articles

View the full record for an article (Abstract or Summary view) and click on the Related Citations link to retrieve closely related citations, based on shared MeSH (Medical Subject Heading) terms.

Review Articles

To narrow your search results to review articles, click on Review in the left-hand column of your search results, under Article types.

Or, from the Advanced Search screen, select Publication Type from the pull-down Search Builder menu. Enter Review in the Search Builder box, then click Add to Search Box. Enter any additional search terms, then click Search.

Search Details

The Search Details box is located on the bottom right side of the search screen. Search Details shows how each search term was translated using PubMed's search rules and syntax. It is useful to understand PubMed's automatic term mapping and search rules. Learn more in Advanced Search Techniques.

RSS Feeds

You can save your searches as RSS (Really Simple Syndication) feeds by running a search in PubMed, and click on the RSS LINK located above the search box. Once the feed is created, copy and paste the URL into the subscribe form in your RSS reader. Click here to read more about RSS feeds and RSS readers.

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Advanced Search Techniques

Advanced Search

On the Advanced Search screen, you can use the Search Builder tool to specify the exact fields for your search terms (author, affiliation, journal title, etc.). You can also access your search history and view and combine past searches. Searches remain in your search history for up to eight hours.

Combine searches or add additional terms to an existing search by using the pound sign (#) before the search number, e.g., #2 AND (#6 OR #3) AND microarray, or re-run a previous search.

Filters

Click on the Show additional filters link to see a list of filters. Using filters you can restrict your search by publication date, language, article type, and many more criteria. Filters remain in effect until you click again on a specific filter to remove it, or click Clear all on your search results screen; filters other than language or date will exclude records in process.

Field Tags

Use PubMed's search field tags to refine your search strategy; enter your search term, qualified with the appropriate search field tag. Below is a list of some of the more frequently used PubMed search field tags with examples of how to use them. A complete list of search field tags is available in the Search Field Descriptions and Tags section in PubMed Help.

Common Field Tags

Affiliation [AD]
Author [AU]
Journal Title Abbreviation [TA]
Language [LA]
MeSH Terms [MH]
Personal Name as Subject [PS]
Publication Date [DP]
Publication Type [PT]
Subset [SB]
    AIDS = aids [sb]
    Bioethics = bioethics [sb]
    Complementary and
    Alternative Medicine = cam [sb]
    History of Medicine = history [sb]
    Toxicology = tox [sb]
Text Words [TW]
Title Words [TI]

If you prefer not to use field tags, go to the Advanced Search page and use the Search Builder to specify specific fields for your search terms.

MeSH Terms [mh] or [majr]

NLM's Medical Subject Headings (field tag: [mh]) are a list of biomedical terms which are used to describe the subject of each journal article indexed in MEDLINE. The [majr] tag retrieves all MeSH terms that are marked as being of major importance in an article. Use either search field tag to search.

Note: Searching with only MeSH terms will exclude  "records in process" citations as they have not yet been indexed with MeSH.

Explode Feature

MeSH terms are automatically exploded by PubMed; that is, all terms which are logical subsets of the term entered are also included. For instance, vision disorders includes blindness. If you want to turn off the automatic explosion, enter the MeSH term in the search box and qualify it with [mh:noexp].

MeSH Database

This is another approach to advanced searching. Look up official MeSH terms to view hierarchical relationships to other subject headings and subheadings.

Single Citation Matcher

When you have all the citation information for a specific article you want to find in PubMed, use the Single Citation Matcher tool. From the main entry page of PubMed, choose Single Citation Matcher (under PubMed Tools). Enter as much or as little of the citation as you wish; journal titles may be entered in full or as abbreviations.

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Finding Full Text and Call Numbers

Full-text linking options are available in the Abstract display; click on an article title to see its full record, including full-text links. Many records in PubMed include a link to the publisher's website, which may take you to the full text. Click the UC-eLinks button for more complete retrieval options: UC-eLinks provides access to the electronic full text of the article (when available), checks for a print copy in the Melvyl catalog, and allows you to Request articles which UC Berkeley does not own.  

Note: You must use the UC-customized PubMed URL (http://uclibs.org/PID/17708) in order to see UC-eLinks buttons!

Click here for more information about using UC-eLinks in PubMed.

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Viewing Citations

Check the boxes to left of each article title to select specific citations. The selected citations can be emailed, saved as a text file, displayed in a different format, or added to the Clipboard by clicking on the appropriate button on the action bar.

PubMed_display

PubMed's default display on the search results page is the Summary format. Click on the title of any article to view it in the Abstract format, which shows links to full-text content. Citations can be viewed in four other formats. You may select another format and/or show more than 20 citations per page by using the Display Settings pulldown menu.

Summary display:

Basic citation information, links to related citations, and PMID (PubMed Unique Identifier). The Summary (Text) display gives only the citation information and PMID, in plain-text format. The Summary displays do not show links to full-text content.

Abstract display:

Article abstract, links to full-text content, MeSH terms, citation information, links to related citations, and PMID (PubMed Unique Identifier). The Abstract (Text) display gives only the citation information, abstract, and PMID in plain-text format.

MEDLINE display:

Choose this display to format your citations for downloading to reference management programs such as RefWorks or EndNote.

Other displays:

Choose XML to see your citations in XML markup format. Choose PMID List to see a list of all the PMIDs (PubMed Unique Identifier numbers) from your selected citations.

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Saving Citations

By clicking on the Send to pulldown menu, your selected citation(s) can be saved to your desktop as a text file, saved temporarily in your Clipboard, or saved permanently in MyNCBI Collections. You can also email or print the citations.

sendto

Clipboard

Use the Clipboard to collect selected citations from one search or several searches, for emailing, saving, printing, or exporting to a citation management program. Once you have selected citations from your search results, add them to the clipboard by selecting Clipboard from the Send to pulldown menu. After adding items to the Clipboard, you can click on the Clipboard link (top right corner of page) to view your selections.

Up to 500 items at once can be stored on the Clipboard. Clipboard items will be lost after eight hours of inactivity.

Collections

Search results from databases can be saved in My NCBI using the Collections feature. With My NCBI you can save searches and data important to you, and set your preferences for NCBI’s tools and web site. Creating a My NCBI account is free to all users.

Email

You can send up to 200 citations at a time through email.

Exporting citations to a reference manager

In your search results, use the check boxes to select citations. You may move to other pages to continue your selections. If you do not make any selections, you will be able to choose how many records will be saved (up to 200).

To export citations into a reference management program such as EndNote or RefWorks:
  1. In your search results, use the citation check boxes to select citations. To export all records, do not select any.
  2. From "Send to", select Citation manager.
  3. Select the number of records and the starting record from the menu and click Create file.
  4. Download this file to your computer, and import it into your reference management program.

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Exporting to RefWorks or EndNote

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Copyright © 2014 The Regents of the University of California. All rights reserved. Comment Form. Last update: 11/12/13

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