Albany Medical College

Schaffer Library of Health Sciences

PubMed
2015

Objectives
By the end of this tutorial, students will be able to do the following in PubMed:
Select appropriate search terms
Perform a basic topic, author, and journal search
Utilize the MeSH Database to select terms and subheadings
Apply limits and Boolean Operators to broaden and narrow search results
Access full-text journal articles
Use My NCBI to save searches
Save, print, and e-mail search results

PubMed @ a Glance

PubMed provides free access to MEDLINE, an international biomedical

database, that is developed and maintained by the National Center for
Biotechnology Information (NCBI), at the National Library of Medicine (
NLM), located at the National Institutes of Health (NIH).
It is one part of NCBIs Entrez life sciences database, which allows
simultaneous searching across multiple databases
It contains more than 24 million citations from journals worldwide
covering the fields of medicine, nursing, dentistry, veterinary
medicine, pre-clinical sciences, and more
Primary coverage dates back to 1948. While some older references
are searchable in PubMed, an index of medical journal articles back to
1879 is available in the Librarys print collection in Index Medicus
Most records are from English language journals

Note: While searchable through www.pubmed.gov, accessing

PubMed through Schaffer Librarys links provides access to
thousands of additional full-text articles.

PubMed Homepage

The homepage contains the Search Box for performing basic

searches in PubMed. Below this box is a link to the Advanced Search
page, which allows for more refined searching options. Click Help at
any time to look up information on searching PubMed and its features.

PubMed Features

Located beneath the Search Box are other search options. Using
PubMed is where you will find help guides, tutorials, and other
general information about PubMed. Choose from PubMed Tools to
perform more guided searches. The More Resources section
includes links to the MeSH Database, Journals Database, and more.
These will be addressed further on in this Tutorial.

A Bit About Boolean

When including more than one term in a PubMed search, it is important to keep
Boolean Operators in mind in order for a search to work properly. The main operators
are AND, OR, NOT.

AND
Use AND between terms when all of them must be included in a citation
Example: otitis media AND antibiotics. This narrows the search
Note! PubMed automatically assumes searchers want the AND operator between
multiple terms, so typing otitis media antibiotics will retrieve the same results. It
is a matter of personal preference whether or not to type the AND operator
OR
Use OR between terms when at least one of the terms needs to be included in a
citation
OR is helpful for synonyms
Example: heart disease OR congestive heart failure. This broadens the search
NOT
Use NOT to exclude a term from the retrieval
Example: anxiety NOT depression. This narrows the search
Note! Use NOT sparingly, as it may eliminate some relevant references. It is
best reserved for use in combining search sets to avoid duplication

Basic Search

PubMed will decipher any search terms typed into the search box
naturally as having the Boolean operator AND between them. So for
the above example, PubMed would find citations with sleep AND
walking AND causes in each of the results.

Basic Search - Results

Results in
brackets indicate
the article is in
another language

Here is an example of the results page. An advantage of searching PubMed

through the Librarys Database page is that a filter appears on the right side of
the page which will instantly limit results to either full text articles available
through Schaffer Library or those that are freely available. The AMC Library
filter will bring up references that have access to full text either through the
Librarys online journals (blue icon) or the Librarys print collection (maroon
icon).

Basic Search - Abstract

In the Abstract view, if the library has a subscription to the journal, the
Schaffer Library Full Text Article icon will be located on the right of the
screen. If the icon doesnt link to the full text of the article please check
the Librarys E-journals page using the citation found above the title of
the article.

Full Text Links

Many references in PubMed provide a link to the journal publishers

website. However, some full-text articles are only accessible through a
Library subscription.
Note that while some full-text journals are freely available by going directly
to pubmed.gov, it is a much smaller number than those available when
accessing it through the Library
If there are no full text links to a desired article, check the
Librarys E-journal page or the online catalog, for print availability. If the
article still isnt available, it may be requested through the
Librarys Request It! service at no charge.
Below are a few types of article icon links that may appear
citation:
Links toinFTathrough
the
Librarys online journals
FT is available in print
journal collection. Click to
see holdings and location
Links to publisher site for
free access. Note that some
publisher icons will appear
but wont provide free
access
Article available through
PubMed Central, a free
NIH digital archive

Basic Search - Indexing

To find out how the article was indexed (MeSH Terms will be explained later
in this tutorial) click on the link Publication Types, MeSH Terms, Grant
Support located below the abstract in the Abstract View. This link is only
available for abstracts that that are indexed for MEDLINE.

Basic Search Related

Citations

Another good source for expanding your search is with Similar

articles. Similar articles are a list of articles similar in scope to the
article abstract currently displayed.

Advanced Search

Up to now weve discussed basic searches, an advanced search requires more use
of the Boolean operators. The example above is that of an advanced search.
When using abbreviations, use the Boolean OR operator and the full text of the
abbreviation. Not all abbreviations are indexed in PubMed.
If combining ORd terms with additional term(s), enclose the ORd terms in
parenthesis and use the Boolean AND to combine the search. The parenthesis
separate the different units of the search.

Results Screens

Results are displayed in Summary format with 20 results per page.

The results view can be changed by selecting different options and
number of results per page from the Summary, per page, and Sort by
dropdowns.

Results Screens

There are two ways to view the Abstract of a record in PubMed.

Either change the Summary Settings to Abstract or click on the
title link.

Results Screens
Abstracts)

(Structured

PubMed now has Structured Abstracts. Not all the abstracts currently
available are structured. Those that are structured will have bolded
section labels such as, background, objective, methods, results, and
conclusions.

Results Screens

(Images)

Abstracts from PubMeds Central articles now have thumbnail

views of Images available. The Images are located at the
bottom of the abstract and may be viewed by mousing over or
clicking the desired image.

Books
PubMed has selected online books available from the NCBI
Bookshelf. MeSH (Medical Subject Headings) is not available for
books or book chapters. MeSH will be explained later in this
tutorial.

Books

(cont.)

Book chapters can be selected right from the abstract.

entire book, click on the image of the book.

To select the

Author Search and Results

Alternative Author Search

Another way to search for an author is in PubMed Advanced Search

Builder. Choose Author from the drop down options and type in last
name first initials. PubMed Advanced Search Builder will be
explained later in this tutorial.

Journal Search &

Single Citation Matcher
A brief overview of how to search for a journal, as well as how to
use the Single Citation Matcher, are addressed in the
following PubMed video. Click link below to view:
Search for a Journal (including Single Citation Matcher)
(2 minutes)
http://www.nlm.nih.gov/bsd/viewlet/search/journal/journal.html

Source: PubMed Quick Tours

http://www.nlm.nih.gov/bsd/disted/pubmed.html

Single Citation Matcher

Single Citation Matcher can be used not only to search for all articles in
a journal but also for specific journal articles. Author, subject, volume,
date, first page, journal title can all be used to help locate an article.

Search Using the MeSH

Database

MeSH (Medical Subject Headings) is the controlled vocabulary that

NLM (National Library of Medicine) uses to index articles in PubMed.
MeSH terms can be found by searching the MeSH Database.

Search Using the MeSH

Database

There are two ways to search using the MeSH Database. One is to use
the link located under More Resources and the second is to choose MeSH
from the PubMed dropdown box.
A third way to search using MeSH terms is by using the Advanced
Search Builder that will be shown later in this tutorial.

Search Using the MeSH

Database

Going back to our basic search example, a search for sleep walking displays the full MeSH
record titled Somnambulism. From this page you may select subheadings, restrict to MeSH
Major Topic (ex. Somnambulsim would be the main point of the resulting articles displayed),
or opt to choose not to include the term(s) found below Somnambulism (for this example
there are no narrower terms). For more information on using MeSH, please view the tutorial
in the next slide.

MeSH (Subject Headings) and

Subheadings
This video describes MeSH (Medical Subject Headings), the controlled
vocabulary used to index articles in PubMed. Click links below to view:

Use MeSH to Build a Better PubMed Query (3 minutes)

https://www.youtube.com/watch?v=uyF8uQY9wys

Sources: PubMed Quick Tours

http://www.nlm.nih.gov/bsd/disted/pubmed.html

Details

Search Details lists out all the ways PubMed searched the topic. Using our basic
search example, sleep walking causes was searched first in MeSH (Medical Subject
Headings) and then in All Fields.
The Search Details box can be found on the right hand side of the main results page.

Details

Notice that because we did not limit our search to MeSH terms only, the results
display both articles that are indexed and those that are not. If we had limited our
search to only MeSH terms, only those articles that were indexed would have
displayed and we would have missed potentially vital results.

Filters
This video describes Filters/Limits, used to narrow search results
in PubMed. Click links below to view:

PubMed: The Filters Sidebar (2 minutes)

http://www.youtube.com/watch?v=696R9GbOyvA

Sources: PubMed Quick Tours

http://www.nlm.nih.gov/bsd/disted/pubmed.html

Subject Filters

Using the Topic-Specific Queries under the PubMed Tools section on the PubMed
homepage limits a search to a specific topic. Two examples of subject filters are
Complementary Medicine and Dietary Supplements.

Subject Filters

Running a search with the selected subject filter of Complementary Medicine

limits the results to only those discussing use of complementary medicine.

Subject Filters

Another way to limit your search to a specific topic is to open the Subjects filter
on the left side of the search results page and select a specific subject or
subjects.

Filters

Note: Filters will remain from search to

search until changed or cleared manually.

Advanced Search Search

Builder & Search History
A brief overview of the advanced search search builder and search
history are addressed in the following PubMed video. Click link below to
view:
PubMed Advanced Search Builder (2 minutes)
http://www.youtube.com/watch?v=dncRQ1cobdc

Source: PubMed Quick Tours

http://www.nlm.nih.gov/bsd/disted/pubmed.html

Advanced Search Search

History

Search History keeps a complete record of each search with the time and
number of results found. Each search is numbered and may be combined
with another search to retrieve a more relevant group of results.
The searches will be saved in Search History for eight hours before they are
automatically cleared. To save the search history longer, use the My NCBI
feature, which was briefly mentioned in the Advanced Search Builder and
History video on the previous slide. My NCBI will be explained later in this
tutorial.

Send To Features

The ability to save or send results are all available from the Send To
dropdown box.
Clipboard saves to the computer for up to 8 hours
Collections and My Bibliography save to a My NCBI account
indefinitely (My NCBI will be discussed later in this tutorial)
E-mail allows selected results to be sent to an email account
File allows selected results to be saved as a text file on your computer
Citation manager allows selected results to be sent to a Bibliographic
Management tool such as EndNote

Send To Features (cont.)

Here is the full display for selecting E-mail as the Send To Feature. The
entire e-mail address is needed for the selected results to be sent. i.e.
DoeJ@mail.amc.edu
200 citations is the maximum amount that can be e-mailed at one time. 20
citations is the default number.

My NCBI

My NCBI is a central place to save personal data and to set up customized search
options
Use My NCBI to:
Save searches and references indefinitely
Set up e-mail alerts for new relevant content on your topic
Set up a personal bibliography (My Bibliography)
Select filters to customize search results, such as highlighting search terms
A short registration form is required to begin using this free service. Click Sign In
To NCBI from top tool bar on PubMed screens to register and sign in.
For more information on My NCBI view the tutorials located under Using PubMed
on the PubMed homepage

Note:
At the end of many of the video tutorials throughout this module you are
directed to Write to the Help Desk for any comments or questions. This
link will direct you to a form to contact the National Center for Biotechnology
Information (NCBI).
Instead, I would like to direct you to contact the Library with any comments
or questions you may have. We are here to help you with your information
needs!

Schaffer Library Reference:

Phone: 262-5532
Email: library@mail.amc.edu

Youve reached the end of the Tutorial!

Final Test:

Click the Test link on sidebar of the LMI 1444 15-16

Sakai site to take the test.
The Test is due 11:59pm, Tuesday, September 1.

Formative Assessment:

Follows after this slide

The formative assessment is for your benefit so
that you are aware you are studying at the level
expected of you.
There is no grade for the formative assessment and
it is open for the rest of the year so that you can
always refer back to it if need be.

Formative Assessment: PubMed

Answer
2

Question