This lecture illustrates how to search PubMed using keywords, advanced search, clinical queries and MeSH terms. Also, different options are displayed to save, email, export to a citation manager and share hits. Researchers could save search strategies either to a temporary storage (e.g. clipboard) or to a permanent storage (e.g. Collections and bibliography).

1. Dr. Iman El Sayed
MSc, Ph.D, Assistant professor (Lecturer) of Medical Statistics, Evidence synthesis
and Systematic Reviews.
Medical Research Institute, Alexandria University, Alexandria, Egypt.
Email: Eman.abd.elftaah@alexu.edu.eg
www.linkedin.com/in/imanelsayed83

2. NATIONAL LIBRARY OF MEDICINE [NLM]

5. Part of the National Institutes of Health
(NIH)
The world’s largest biomedical library; it
produces:
i. PubMed = Index to world’s
biomedical literature
ii. MedlinePlus = Patient education &
consumer health information
NATIONAL LIBRARY OF MEDICINE [NLM]

6. iii. ClinicalTrials.gov = Database of
clinical trials
iv. TOXNET = Databases on toxicology,
hazardous substances, environmental
health, etc.
And much more
NATIONAL LIBRARY OF MEDICINE [NLM]

7. The world’s largest biomedical
database
Covers all aspects of biosciences and
healthcare
MEDLINE

8. The primary component of
MEDLINE

9. What’s PubMed?
An Online database developed by the NLM,
providing FREE access to MEDLINE records.
PUBMED

10. Biblographic database
(Library)
Online access to MEDLINE
Summing It UP

11. Accessing PubMed
www.pubmed.gov
http://www.ncbi.nlm.nih.gov/pubme
d/
Or
[National Centre for Biotechnology
Information]

12. HELP:
http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/
http://www.who.int/hinari/training/module_4_PubMed/en/

13. A search box where
you enter your terms
Search
Features

14. Automatic Suggestion
feature will display as you
type in your search and it
may be temporarily
switched off by clicking on
‘Turn Off’.
Search
Features

15. Search
Features
A Database selection
menu, Where you can
choose between PubMed
and other NCBI
databases

16. Search
Features
A link to limits, where
you can add criteria
to narrow your
search
A link to Advanced
Search

17. BASIC SEARCH: BY AUTHOR
There are three ways to search by
author:
I. Enter the author’s last name and initials in the
search box
II. Use advanced search
III. Use single Citation Matcher

18. Basic Search: By
Author
To Use Pubmed to
Search By an
author, Type in the
Author’s last name
and initials, use No
punctuations
PubMed retrieves authors
with the last name and
initials used in the search
Some authors are found by the
full name but it is more
comprehensive using the
author’s name and initials

19. Basic Search: By
Author II. By Advanced Search

20. Basic Search: By
Author II. By Advanced Search
Use the auto
complete feature to
find the closest
match
Use the search
builder to choose to
search by Author

21. Basic Search: By
Author III. By Single Citation Matcher

22. Basic Search: By
Author III. By Single Citation Matcher

23. Basic Search: By
Author III. By Single Citation Matcher
Notice the number
of results

24. Basic Search: By
Author III. By Single Citation Matcher
Notice as well the
two choices

25. Basic Search: By
Author III. By Single Citation Matcher
Displayed results
showing only
citations where the
author is the first
Author

26. Basic Search: By
Author III. By Single Citation Matcher

27. Basic Search: By
Author III. By Single Citation Matcher
Displayed results
showing only
citations where the
author is the Last
Author

28. Basic Search: By
Subject

29. Basic Search: By
Subject

30. Basic Search: By
Subject
Be as
specific as
possible

31. Basic Search: By
Subject
Be more
specific
Still getting too
many results we
can use the limits
feature

32. Basic Search: By Author &
Subject
To combine an author
and subject search,
type in the search box
the author ‘s last name
and initials, and
subject terms. you
don’t have to use
‘’AND’’

33. UNDERSTANDING SEARCH
RESULTS
I. Title of the article
II. Author’s Name
III. Source: Provides the journal title
abbreviations, date of publication, volume,
issue, and page numbers of the article

34. UNDERSTANDING SEARCH
RESULTS
IV. PubMed Identifier
V. Tags
VI. Related Citation

35. UNDERSTANDING SEARCH
RESULTS
VII. Free PMC Article: The availability of
free full text from PubMed Central is
indicated

36. UNDERSTANDING SEARCH
RESULTS
Move the mouse over of the journal title
abbreviation displays the full journal title

37. UNDERSTANDING SEARCH
RESULTS
PubMed status tag types:
I. As supplied by publisher
An accelerated method to obtain citation
electronically transmitted through the publisher, to
have access to articles very quickly

38. UNDERSTANDING SEARCH
RESULTS
PubMed status tag types:
II. In process
Provide basic citation information and abstract
while
the subject is being reviewed for accuracy and if
the
scope of the subject is related to MEDLINE.

39. UNDERSTANDING SEARCH
RESULTS
PubMed status tag types:
III. Indexed for MEDLINE
After Medical Subject Headings (NLM's controlled
vocabulary
terms) and other indexing terms are added, the In Process
citations graduate to MEDLINE records. These "completed"
records have also been checked for bibliographic accuracy

40. UNDERSTANDING SEARCH
RESULTS
Related Citation

41. UNDERSTANDING SEARCH
RESULTS
Related Citation
PubMed uses a powerful word algorithm to
compare words from the Title and Abstract
of each citation, as well as the MESH
headings assigned. The best matches for
each citation
are pre-calculated and stored as a set

42. UNDERSTANDING SEARCH
RESULTS
Related Citation
You may see a few citations without the
Related Citations link, which simply means
that these citations have not yet gone
through the algorithm

43. Related
Citation

44. Author’s name
Author’s Address
Abstract of the
published article
Preview of the images
in the article from
PubMed CentralLink to related
resources in external
sources
LinkOut Icons
Links to Related Citations
Links to related resources in NCBI
database
Understanding
Abstract

45. Search Details

46. Search Details

47. Search Details

48. Search Details

49. Limiting A Search: Use
Limits

50. Limiting A Search: Use
Limits

51. PubMed identifies
17578 articles
Limiting A Search: Use
Limits

52. Limit to articles that are
Clinical trials, human studies and
written in English
Limiting A Search: Use
Limits
Click Search

53. A yellow triangle will be displayed
at the top of the results screen
when limits have been set
Results are reduced
from 17578 to 1913
Limits can be removed or
changed
Don't forget to "remove" your limits
before beginning a new search
Limiting A Search: Use
Limits

54. PubMed Tools: Single Citation
Matcher

55. PUBMED TOOLS: SINGLE CITATION
MATCHER
A tool for locating a specific article of
interest
Allows you to track down a paper when
you do not have the full details
The fewer details you provide, the greater
will be the number of articles found

56. PubMed Tools: Single Citation
Matcher

57. Batch Citation Manager

58. PubMed Tools: Top-Specific
Queries

59. PubMed Tools: Top-Specific
Queries

60. PubMed Tools: Top-Specific
Queries

61. PubMed Tools: Top-Specific
Queries

62. PubMed identifies 20articles
PubMed Tools: Top-Specific
Queries

63. PubMed Tools: Top-Specific
Queries

64. Limits have been set to
AIDS subset only
PubMed Tools: Top-Specific
Queries

65. PubMed Tools: Clinical
Queries

66. PubMed Tools: Clinical
Queries

67. PUBMED TOOLS: CLINICAL
QUERIES
When a search is run, a filter is
applied to the search results to focus
on a particular aspect
PubMed Clinical Queries contains 3
parts:
I. Clinical study category
II. Systematic reviews
III. Medical genetics

68. PubMed Tools: Clinical
Queries

69. PubMed Tools: Clinical
Queries

70. PubMed Tools: Clinical
Queries
Narrow (specific
search)
Broad (Sensitive
search)

71. PubMed Tools: Clinical
Queries

72. ADVANCED SEARCH
Advanced search link provides two options
to refine and focus a search, a Search Builder
and a Search History
For Building, Combining and saving search

73. Advanced
Search

74. Search Builder to build
search
Search history to combine
search
Advanced
Search

75. My
NCBI

76. To add or remove windows on
the My NCBI homepage
My
NCBI

77. My
NCBI

78. MY NCBI: SEARCH RESULTS
STORAGE
A. Temporary Storage: Save to
Clipboard
B. Permanent Storage

79. MY NCBI: TEMPORARY STORAGE
Temporary Storage: Save to Clipboard
The Clipboard lets you temporarily collect
selected citations for later action
This feature allow collections of selected
citations from one or more searches for
saving, printing, e-mailing, ordering or
storing in My NCBI

80. Click add to Clipboard
My NCBI: Temporary
Storage

81. My NCBI: Temporary
Storage

82. The Clipboard link is
available on the PubMed
homepage only when items
are stored on the Clipboard
My NCBI: Temporary
Storage

83. MY NCBI: PERMANENT STORAGE
Permanent Storage
I. To save Clipboard items permanently, use
the send to drop-down menu and select
E-mail, File(Save to you computer) or
Collections(to add item to an NCBI
collection)

84. MY NCBI: PERMANENT STORAGE
Permanent Storage
II. To save search queries for NCBI
databases,
and provides automatic e-mail updates for
saved searches

85. My NCBI: Permanent
Storage
Click Search

86. My NCBI: Permanent
Storage
Click “Save
Search”

87. My NCBI: Permanent
Storage
Rename your
search

88. My NCBI: Permanent
Storage
Click ‘’Save’’

89. My NCBI: Permanent
Storage
Set e-mail updates
option(s) then click
save

90. My NCBI: Permanent
Storage

91. MY NCBI: COLLECTIONS
Use My NCBI Collections to save PubMed
citations for future use in PubMed
Save citations to a permanent Collection
from search results, Clipboard or recent
activity
Save citations temporarily using the
Clipboard or permanently using My NCBI
collections

92. My NCBI:
Collections
Click Add to
Collections

93. My NCBI:
Collections
Add selected items to
a new collection or to
an exciting collection
then click Save

94. My NCBI:
Collections
Click the gear icon to
edit a collection
By default, all
collections are set to
Private

95. My NCBI:
Collections
You can download
results into different
formats
Make you citation
Public to be shared
with others
Click on Edit Settings to
get the URL to share

96. My NCBI:
Collections

97. MY NCBI: FILTERS
My NCBI includes a filters feature which
groups search results by area of interests
Two filters appear by default when you
search pubMed: Free Full Text and Review

98. My NCBI:
Filters
To add or remove
filters

99. My NCBI:
Filters

100. GETTING ARTICLES
 PubMed doesn’t include Copies of Journals, yet it offers
LINKS to full text of journals
Links to full text resources from PubMed are available
through a service called LinkOut

101. GETTING ARTICLES
Accessing to Full Text Through:
i. Filters
ii. PubMed Central
iii. Publisher offering free or pay per view access
iv. NLM Loansome Doc(Document Delivery service)
v. Institutional Libraries that are affiliated

102. iv. Loansome Doc
Select articles you want to order, click
on send to and select ‘Oder’, Order
articles icon will take you to the
loansome Doc page
Getting Articles
[LinkOut]

103. Getting Articles
[LinkOut]

104. MeSH database
MeSH is the controlled vocabulary for indexing articles for
MEDLINE. MeSH Terms are assigned as Keywords to each
record that is “Indexed for MEDLINE”.
In MeSH, we will complete a
search for the term Malaria.

105. From these results we note
that the MeSH has listed 9
terms for Malaria.

106. We have checked the box for
the first for Malaria result from
the MeSH search.

107. After clicking on Malaria, we will
open the Display Settings drop
down menu, click on the Full
button and Apply.

108. The record for a MeSH term (Malaria) contains the
definition, associated subheadings, a list of entry
terms, and the tree view of MeSH.
Highlighted is the definition provided for Malaria.
Note the subheadings listed on this page.

109. For each MeSH term, Entry
Terms also are listed along
with See Also references.

110. To complete a PubMed search with the
Malaria MeSH term, we first will click on
Add to search builder and then click on
Search PubMed.
Note how “Malaria[Mesh]” is displayed in
the PubMed search builder box.

111. We have displayed PubMed search
results for the Malaria[Mesh] term. Note
that there are 12532 Free Full Text
articles.