PubMed/How to Search, Display, Download

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PubMed/How to Search, Display, Download Email
(module 4.1)



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MODULE 4.1PubMed/How to Search, Display,
Download Email

• Instructions - This part of the
• course is a PowerPoint demonstration intended to
  introduce you to PubMed/How to Search, Display,
  Download Email
• module is off-line and is intended as an
  information resource for reference use.

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Table of Contents

• Connecting to PubMed
• Navigating through PubMed
• Selecting a database to search on the black
  database bar
• Searching PubMed
• Query Translation
• Display options
• Printing, saving and email options

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Logging on to HINARI 1
Before logging into PubMed, we can Login to the
HINARI website using the URL http//www.who.int/hi
nari/
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Logging into HINARI 2
We will need to enter our HINARI User Name and
Password in the appropriate boxes, then click on
the Login button. Note If you do not properly
sign on, you will not have access to full text
articles.
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Remember - if you fail to use the Login page, you
will have a second option on the Full text
journals, databases, and other resources
sub-page.
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Main HINARI webpage
Once you are logged in from the main HINARI
webpage, access PubMed by clicking on Search
HINARI journal articles through PubMed (Medline).

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PubMed home page 1
Welcome to the PubMed Homepage. Part 1 of the
tutorial will look at the interface, display
options, downloading and emailing results.
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Other NCBI databases
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.
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NCBI OMIM database
Here is the OMIM database. To return to PubMed,
click on the link on the database bar.
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PubMed home page 2
Down the left column of the PubMed homepage,
there are links to other PubMed resources
including Overview to PubMed, Help Frequently
Asked Questions, Tutorials and News items.
Down the left column of the PubMed homepage,
there are also links to other PubMed Services
including Journals Database, MeSH Database,
Clinical Queries, LinkOut and Citation functions.
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PubMed home page 3
The Search box on PubMed is active. Type here to
enter your search statement.
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PubMed search box
In this example we will enter a search for
malaria infections in Africa into the Search or
query box. To execute the query, click on the Go
button.
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Results - default display
Results of the search are displayed in the main
body of the page. Note the two additional tabs
for Free full text and HINARI articles. These are
MyNCBI searches that are included in all the
HINARI/PubMed queries (see module 4.5). Of the
3223 articles, 1274 are available via the HINARI
tab and 843 with Free full text tab ( there is
some overlap).
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The Details link
To see how PubMed performed the search, we can
click on the Details link highlighted below the
query box.
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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.
Details
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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, or Medline. The other formats are for
different NCBI databases. We have selected
Summary from the available options. To change the
Display, click on one of the options in the drop
down menu.
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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. Records 1-20 out of 3223 are
displayed on this screen. Note the Free articles
in PMC / at journal site hypertext link. This
link will lead directly to the free full text
article from the Summary display.
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Brief format
From the drop down menu, we now will select the
Brief Display option.
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Brief format 2
The Brief Display shows the name of the first
author, part of the article title, and the PubMed
ID number.
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Abstract format 1
The Abstract option now is highlighted.
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Abstract format full text links
The Abstract Display option will show any links
to publishers websites which may have the full
text available. In this example we have a link to
Wiley InterScience and next to this is the
HINARI icon which identifies access rights for
HINARI registered institutions.
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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.
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AbstractPlus Example
This is an example of the AbstractPlus Display.
Note the relocation of the HINARI and Elsevier
icons.
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Citation format 1
The Citation Display option is similar to the
abstract display but has some extra information
such as MeSH terms and substances included (for
articles completely indexed in MEDLINE).
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Add citation here!
In the Citation display option, we can see the
MeSH Terms assigned to the record during indexing
by the National Library of Medicine (NLM). Also
note the HINARI icon to the full-text article.
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MEDLINE format 1
The MEDLINE Display option is selected here.
The MEDLINE Display option is selected here.
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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.
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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 Show drop down menu, 200 has
been selected to re-display. To change the Show
number, click on one of the options in this menu.
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Results pages
The results page is now displaying 1-200 of 3223
citations. There are now only 17 pages of results
to view.
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Sorting options
Results can be ordered alphabetically by Author
or Journal title, or by publication date (the
default). In this example, Journal has been
selected from the drop down menu. To change the
display's sort format, click on one of the
options in this menu.
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Sorting by journal title
The results 1-200 are now displayed
alphabetically by Journal title.
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Selecting references
To select references from the results list, we
need to check the box on the left side near the
top of each record. This is required for the
Send to Text, Print, Save or Email options.
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Selecting references 2
From the results page, records 1-5 now have been
selected.
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Send to Text option 1
The results selected can now be formatted for
print by selecting Send to Text from the drop
down menu.
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Send to Text option 2
This option presents a format for output to a
printer.
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Send to File 1
To download selected results to a hard drive,
floppy disk, compact disk or flash drive, select
Send to File from the drop down menu.
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Send to File 2
Open the file in Notepad and give it a .txt file
extension. Click on Save File.
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Send to Email 1
To email selected results, choose Send to E-mail
from the drop down menu.
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Send to Email 2
Type in an email address in the box provided.
Then click on the Mail button. Note that we have
selected the Abstract Format as HTML and Sorting
by Pub Date.
From this screen, we can choose a format and
sorting order, and add text notes.
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Send to Email 5
When you return to the main results screen, a
message bar appears to inform that an E-mail has
been sent from the PubMed server to the client
address.
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This is an an example of an E-mail received from
PubMed. The four citations that were checked are
in the Abstract display.
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Send to Clipboard 1
Selected results can also be sent to a clipboard
area. Select Send to Clipboard from the drop down
menu.
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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.
Since we checked 5 items, these have been
transferred to the Clipboard.
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Send to Clipboard 3
To retrieve items from Clipboard, click on the
link below the query box.
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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. Here, we have the
Abstract display.
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Send to Clipboard 5
To remove an item from Clipboard, choose Send to
Clip Remove from the drop down menu.
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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. There is a
workbook 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. Updated 06
2009