Pub Med Explained - BSD Office of Faculty Affairs

PubMed Explained
Improve your PubMed search skills &
Deb Werner
Director of Library Research in Medical Education
[email protected]
 Search PubMed effectively and efficiently through use of:
 An understanding PubMed’s search process
 MeSH
 Clinical Queries
 Manage search results with:
 Find It for full text
 Reference managers
What is the difference b/w PubMed
24M citations
21M citations
5,600 journals
Back to 1940s
3.3M citations with full text
Back as far as 1800s
NIH-funded manuscripts
NCBI Bookshelf
Over 1,300 e-books
Out-of-scope citations
Access PubMed from the
hospital intranet page
Access PubMed from the
Crerar Library home page
Finding Full Text
Accessing PubMed from Crerar or the
hospital provides access to the Find It
button, linking citations to the library’s
full text subscriptions.
Searching PubMed – two ways
1. A quick search to find a few good articles
2. An in-depth search to find comprehensive information
on a particular topic
The quick search
1. Search all relevant terms at once
2. Review results
3. Edit search if necessary
 Review Search Details
 Use different search terms
 Apply Filters
What is MeSH?
 Acronym for Medical Subject Headings
 A controlled vocabulary used to index and search
biomedical information
 Provides uniformity and consistency
 Developed & maintained by National Library of Medicine
 Pros
 Synonyms searched
 Disambiguation of terms
 Targeted results
 Cons
 Newest citations do not have MeSH terms and so not searched
 Some concepts (esp. newer diseases, treatments, etc.) do not have
MeSH terms
 Examples
 Cold could mean temp or virus; MeSH uses “Cold Temperature”
and “Common Cold”
 “Nursing” is the field of nursing, not breast feeding
 “Drinking” is term for consumption of liquids, if looking for
consumption of alcohol, use “Alcohol Drinking”
Keywords (aka text words)
 Pros
Retrieve newest citations
Use natural language
Use current terminology
Useful when MeSH term does not exist for concept
Useful when MeSH term does not precisely represent concept
 Cons
 Ignore context
 Homonyms
 Negating expressions (but, except, never…)
 Treat all words with equal importance
 Synonyms and spelling variations not searched
Some information based on a presentation by Rachel Adams, University of Salford at
Accessing MeSH database
Clinical Queries
Accessing Clinical Queries
The in-depth search
1. Break question into individual topics or concepts
2. For each concept, identify MeSH terms and keywords
3. Combine MeSH and keyword searches to create a “set”
for each concept
4. Combine sets
5. Evaluate results
6. Broaden or narrow search as needed
Identify individual topics
 What are individual concepts our previous question:
Do medical school graduates feel prepared for their
first year being a resident?
 medical school grads/ perception / preparedness / 1st year
Identify MeSH terms & keywords
 medical school grads/ perception / preparedness / 1st year
 In the MeSH database, find MeSH terms for each concept
Students, Medical
Self Concept
Clinical Competence
Internship and Residency
 Brainstorm ideas for keywords
Medical students/undergraduate medical education
Combine MeSH and keywords
 Create a “set” for each concept by combining MeSH and
Students, Medical/undergraduate medical education
Self Concept/perception
Clinical Competence/preparedness
Internship and Residency/residents
 How should these terms be combined?
Combine MeSH and keywords
 Create a “set” for each concept by combining MeSH and
keywords for each concept
Students, Medical OR undergraduate medical education
Self Concept OR perception
Clinical Competence OR preparedness
Internship and Residency OR residents
Combine sets
 Combine the sets to complete the search
 Medical students set AND Perception set AND Preparedness set
AND Residency set
Review your results
 Do your results appear to answer the question:
 Do medical school graduates feel prepared for their first year of
being a resident?
 How many results did you get?
 Too many or too few?
Improving your search
 Too many results?
 Narrow focus or use Filters: date, language, publication type,
 Too few results?
 Expand search with additional synonyms, broader search terms
or by removing some Filters
 Find an article right on target?
 Look at its MeSH terms to identify other potential search terms
 Searching is an iterative process; revise your search
until you are satisfied with the results or satisfied you’ve
done all you can
Caution on using Filters
 Some Filters are actually MeSH terms, including:
Many of the publication types
Age groups
 These Filters restrict results to that parameter and to
indexed articles only (i.e. eliminates the newest citations)
 Filters remain activated for subsequent searches
 My NCBI is a personal account:
 Save searches
 Save citations (not full text)
 Set up search alerts; receive emailed results
Accessing My NCBI account
Account options
Sign in with an existing
Google, NIH or eRA
Commons account.
Register for an NCBI
Managing your results
 Export results to Zotero, Mendeley, EndNote, or other
reference manager to store and organize citations
 Library holds quarterly workshops
 Register at
 Individual or small group consultations available
 Email me at [email protected]