Introduction to PubMed

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Introduction to PubMed

• Your Name
• Your contact information can go here

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Objectives

• Understand the purpose and content of PubMed
• Be able to perform a basic search in PubMed
• Be familiar with PubMeds special features
  Related Articles, Journal Links to Full Text,
  MyNCBI and others

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The National Library of Medicine (NLM)

• Part of the National Institutes of Health (NIH)
• The worlds largest biomedical library it
  produces
• PubMed Index to worlds 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

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MEDLINE

• The worlds 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

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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

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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

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Lets Talk

• and lets do a PubMed literature search using
• Limits
• Related articles
• Display features
• Print and Save features
• Clinical Queries
• My NCBI

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Accessing PubMed

• Directly at http//pubmed.gov
• Or, National Library of Medicines homepage
  http//www.nlm.nih.gov

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PubMed Screen Layout
Query Box aka Search Box
Feature Tabs
Blue Sidebar
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Searching PubMed

• Lets use this search
• Whats the evidence for the use of beta blockers
  to prevent atrial fibrillation after bypass
  surgery

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Enter Your Search in Query Box
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Results Screen
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The Details Tab
Details Tab tells you how PubMed has
translated your search
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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

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Automatic Term Mapping

• arthritis aspirin gastric mucosa
• is automatically translated into
• ("aspirin"MeSH Terms OR aspirinText Word) AND
  ("arthritis"MeSH Terms OR arthritisText Word)
  AND ("gastric mucosa"MeSH Terms OR gastric
  mucosaText Word)

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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

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The Limits Tab
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Other Ways To Limit Your Search

• Add additional terms to query box
• Use Boolean Connectors
• AND, OR, NOTstress AND depressiondepression OR
  sadness OR unhappy depression NOT manic

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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

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Clinical Queries
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(No Transcript)
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Related Articles
Related Articles a pre-formulated search
strategy to match other PubMed citations that are
closely related to the selected citation
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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)

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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

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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

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What Are Those Icons?
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Important Icons

• Free full-text from publishers site
• Registration may be required
• Free full-text from PubMed Central
• Publisher icons that dont indicate FREE or
  subscription

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Another Way to Get the Article

• NLMs 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.h
  tml

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

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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.
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Saved Searches
After 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.
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Additional Resources

• The National Library of Medicine
• www.nlm.nih.gov
• 1-888-FINDNLM (1-888-346-3656)
• custserv_at_nlm.nih.gov
• Your wonderful librarian!