MODULE 4
How to use PubMed
Part 1 – PubMed Interface, Display options, Saving, Printing, and Emailing results.
Instructions
This part of the course is a PowerPoint demonstration intended to show a guided tour
of the PubMed interface.
This part of the module is off-line and intended as an information resource for
reference use.
This part of the module should be taken before using the live tutorial on the PubMed
and does not require a HINARI training password.
HINARI Log-In 1
Before logging into PubMed we can Log In to
the HINARI website using the URL
http://www.who.int/hinari/en/
HINARI Log-In 2
You will need to insert your HINARI User ID and
password in the Log In box and click on the
“Sign On” Icon
Main HINARI’s Journal webpage
Special Link:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=hinari
From the main HINARI webpage you can
access PubMed from the “Find articles” link in
the body of the webpage. Click on Search for
articles through PubMed (Medline).
PubMed home page
Welcome to the PubMed Homepage, Part 1 of
the tutorial will look at the Interface, display
options, downloading and emailing results.
NCBI databases bar
The black bar above the query box contains
links to the other NCBI databases, highlighted
above are the links to PROTEIN, OMIM, and the
PubMed Journals database. To move between
databases Click on the database name.
NCBI – OMIM database
Here is the OMIM database, to return to
PubMed click on the link on the database bar.
PubMed left-hand menu
Down the left-hand side of the
PubMed homepage there are links to
other PubMed resources such as an
overview to PubMed, Help &
Frequently Asked questions, a
Tutorial, and news items.
Down the left-hand side of the
PubMed homepage there are also
links to other PubMed utilities such
as the Journals database, MeSH
database, clinical queries, LinkOut
and citation functions.
PubMed query box
The query box on PubMed is active, type here to
enter your search statement.
How to Query a Particular Database
term1 term2
(term1[tag
delimiter]
op term2[tag
delimiter]
op = AND, OR, NOT
Boolean operators MUST be in ALL CAPS!
tag delimiter
= Entrez indexing field
Text Word
Journal
MeSH Terms
Author
Examples of
tag delimiters
op …)
PubMed simple search
In this example we will enter a search for
“malaria infections in Africa” into the query box.
To execute the query click on the “Go” Icon.
Results - default display
Results of the search are displayed in the main
body of the page.
The Details link
To see how PubMed performed the search we
can click on the “Details” link highlighted below
the query box.
Details page
PubMed uses automatic term mapping. Details
shows how the PubMed software breaks down
the search statement. In this example PubMed
searches for Malaria as a text word and a MeSH
term because of the automatic term mapping.
Africa and Infections are also searched as a text
words and MeSH terms.
Results – display options
Highlighted below the query box are the default
display options. Records are displayed in
Summary format, records 1-20 out of 1599 are
displayed and the Sort order is by PubMed ID
number.
Display formats
There are a number of different
formats available to display results.
From the dropdown menu we can see
the possible choices. When using
PubMed we will use either Summary,
Brief, Abstract, Citation, and Medline.
The other formats are for other NCBI
databases. We have selected
Summary from the available options.
To change the display click on the
“Display” button.
Summary format
The Summary format displays the authors
names, the title of the article, the title of the
source publication with citation details, and the
PubMed ID number.
Brief format
From the dropdown menu we can now select the
“Brief” display option.
Brief format 2
The brief display shows the name of the first
author, part of the article title, and the PubMed
ID number.
Abstract format 1
The “Abstract” Option is now highlighted.
Abstract format – full text links
The abstract display option will show any links to
publishers websites which may have full text available.
In this example we have a link to Elsevier Science and
next to this is the HINARI Icon which identifies access
rights for HINARI registered institutions.
Abstract format – Affiliation information
The abstract display also gives affiliation
information. This affiliation information is for the
first author listed on the paper, NOT all authors.
Citation format 1
The “Citation” display option is similar to the
abstract display but has some extra information
such as MeSH terms and substances listed.
Citation format – MeSH information
Here we can see the MeSH Terms
assigned to the record during
indexing by the National Library of
Medicine (NLM).
MEDLINE format 1
The “MEDLINE” display option is selected here.
MEDLINE field identifiers
The “MEDLINE” display option
shows all the fields in the MEDLINE
record with field identifiers at the
beginning of each line. This format
is best used for downloading
records into reference managing
software.
Number of records displayed
There are a number of different options for displaying the
number of references per page. These range from 5 to 500.
It is advisable to download as many references per page
as possible as this will save time when viewing results by
eliminating the need to scroll through numerous pages.
From the dropdown menu “200” has been selected, to redisplay the results Click on “Display”
Results pages
The results page is now displaying 1-200 of 1599. There
are now only 8 pages of results to view.
Sorting options
The default ordering of results is by PubMed ID number.
Results can be ordered alphabetically by Author or
Journal title, or by publication date. In this example
“Journal” has been selected from the dropdown menu.
To redisplay by Journal click on “Display”.
Sorting by journal title
The results 1-200 are now displayed alphabetically by
journal title.
Selecting references
To select references from the results list you need to
check the box on the left-hand side near the top of each
record.
Selecting references 2
The results page 1-4 have now been selected.
Send to Text option 1
The results selected can now be formatted for print by
selecting “Send To Text” from the dropdown menu.
Send to Text option 2
This option presents a printer friendly
format for output to a printer.
Send to File 1
To download selected results to a disk drive select
“Send To File” from the dropdown menu.
Send to File 2
Select a location to save the file and change the file type
from fcgi document to all files.
Send to File 3
Choose a name for your file and give the file a .txt file
extension. Click on Save
Send to Email 1
To email selected results choose “Send To email” from
the dropdown menu.
Send to Email 2
From this screen you can choose a format
and sorting order, and add text notes.
Send to Email 3
Type in an email address in the box provided.
Send to Email 4
Then click on the “Mail” button
Send to Email 5
When you return to the main results screen a message
bar appears to inform that an email has been sent from
the PubMed server to the client address.
Send to Clipboard 1
Selected results can also be sent to a clipboard area.
Select “Send To Clipboard” from the dropdown menu.
Send to Clipboard 2
An information bar will appear telling you how many
results have been sent to clipboard, the time limit after
which they will be lost, and the maximum number of
items allowed on the clipboard.
Send to Clipboard 3
To retrieve items from Clipboard Click on the link below
the query box.
Send to Clipboard 4
From within Clipboard you can re-format and display
results in the same way as you can from the main
results page.
Send to Clipboard 5
To remove an item from clipboard choose “Clip Remove”
from the dropdown menu.
Send to Clipboard 6
An information bar will appear saying how many items
were removed from the Clipboard”.
This is the end of Module 4 Part 1
This is the end of Module 4 Part 1.
There is a Work Book to accompany this part of
the module. The workbook will take you through
a live session covering the topics included in this
demonstration with working examples.