Introduction to PubMed

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Objectives

Understand the purpose and content of PubMed

Be able to perform a basic search in PubMed

Be familiar with PubMed’s special features: “Related Articles”, “Journal Links to Full Text”, MyNCBI and others

The National Library of Medicine (NLM) Part of the National Institutes of Health (NIH) The world’s largest biomedical library; it produces:

PubMed = Index to world’s biomedical literature

MedlinePlus = Patient education & consumer health information

ClinicalTrials.gov = Database of clinical trials

TOXNET = Databases on toxicology, hazardous substances, environmental health, etc.

And much more

MEDLINE

The world’s largest biomedical database

Over 5,000 journals indexed, with worldwide coverage

Covers all aspects of biosciences and healthcare

Database of 16+ million journal citations, 1950 to the present

90% are in English ; 79% have abstracts

The primary component of PubMed

So What Is PubMed? PubMed is a tool to search:

MEDLINE (1950 to present) In-process & publisher-supplied citations (some before they are published

in hard copy) Citations from some older materials not yet upgraded with

MEDLINE indexing, some out-of-scope articles from MEDLINE journals, and some life sciences journals that submit full text to PubMedCentral

Produced by NCBI National Center for Biotechnology Information, part of

NLM

Accessible worldwide on the Web at no charge

What Is MeSH?

MeSH – Medical Subject Headings Controlled vocabulary terms Hierarchical structure from broad to specific

PubMed translates common terms to MeSH terms Breast cancer = Breast neoplasms Middle ear infections = Otitis Media Heart attack = Myocardial Infarction

Let’s Talk

…and let’s do a PubMed literature search using: Limits Related articles Display features Print and Save features Clinical Queries My NCBI

Accessing PubMed

Directly at: http://pubmed.gov

Or, National Library of Medicine’s homepage: http://www.nlm.nih.gov

PubMed Screen Layout

Feature Tabs

Query Box aka Search Box

Blue Sidebar

Searching PubMed

Let’s use this search:

What’s the evidence for the use of beta blockers to prevent atrial fibrillation after bypass surgery

Enter Your Search in Query Box

Results Screen

The Details TabDetails Tab tells you how PubMed has translated your search

Automatic Term Mapping

PubMed automatically checks what you enter against its indexes in this order:

MeSH Journal Title Author If no matches, PubMed breaks your search terms apart

and searches each piece against these indexes Any term that cannot be matched is searched in ALL

FIELDS

Automatic Term Mapping

arthritis aspirin gastric mucosa

is automatically translated into:

("aspirin"[MeSH Terms] OR aspirin[Text Word]) AND ("arthritis"[MeSH Terms] OR arthritis[Text Word]) AND ("gastric mucosa"[MeSH Terms] OR gastric mucosa[Text Word])

When to Limit?

There are many reasons for refining a search strategy. You may want to:

Exclude foreign language titles

Look for articles published within a certain timeframe

Retrieve articles that focus on specific populations

Look only at clinical research studies

The Limits Tab

Other Ways To Limit Your Search

Add additional terms to query box

Use Boolean ConnectorsAND, OR, NOT

stress AND depressiondepression OR sadness OR unhappy depression NOT manic

Boolean Searching Use AND, OR, NOT and parentheses:

(moose OR elk OR deer OR camel)

AND automobile accidents

Use History Tab to assist in Boolean searching

Clinical Queries

Related Articles

Related Articles – a pre-formulated search strategy to match other PubMed citations that are closely related to the selected citation

Working with Results

The Display bar is used with the following pull-down menus:

Summary lets you select other formats, such as Abstract, Brief or Citation format

Show and Sort By offer additional display options

Send to lets you print, save, e-mail, order documents or the Clipboard (a temporary holding bin)

The Clipboard Tab

Lets you keep track of “the good ones” while you are still searching

How to: #1: Check the citations to keep #2: Use the Send pull-down menu to select Clipboard #3: Repeat with other strategies #4: Click on Clipboard to view your collection

Will keep up to 500 records for 8 hours! More about how to save citations longer when we talk about

MyNCBI

Are the Actual Articles Online?

If and only if: The publisher chooses to make it freely available

on its website.

The publisher has “deposited” content in PubMed Central

You or your library has purchased access to full text online

What Are Those Icons?

Important Icons

Free full-text from publisher’s site

Registration may be required

Free full-text from PubMed Central

Publisher icons that don’t indicate FREE = $$ or subscription

Another Way to Get the Article

NLM’s Loansome Doc Ordering System

A service that allows users to obtain the full-text copies from a medical library

For more information ask your librarian or go to: http://www.nlm.nih.gov/loansomedoc/loansome_home.html

Links to LinkOut

LinkOut – connects you to other related resources, e.g., publishers, NLM resources and other organizations

This PubMed feature allows you to:

Save search strategies and set-up automatic email updates

Save bibliographies Select filters that customize and sort your search

results and more…

Saved Searches

My NCBI box lets you Sign in or for first time users, Register. After a search is run, click on the Save Search link to save the search strategy.

Saved SearchesAfter you sign in, the Save Search box displays. 1) Enter a name for your search (something meaningful), 2) click Yes or No for automatic e-mail updates and 3) click OK after you have made your selections.

Additional Resources

The National Library of Medicine www.nlm.nih.gov 1-888-FINDNLM (1-888-346-3656) custserv@nlm.nih.gov

Your wonderful librarian!