PubMed/How to Search, Display, Download & Email

(module 4.1)

MODULE 4.1

PubMed/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.

Table of Contents

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

Before logging into the Partner Publisher services websites, we will Login HINARI site using the URL to the http://www.who.int/hinari/

You need to enter your HINARI User Name and Password appropriate boxes, then click on the Login button. To have access to the full text articles, you must properly sign in.

in the If you do not use the Internet Explorer Web browser, this slide will not appear (as of 01 April 2014). If you use Internet Explorer, you will continue to have a two-step login process.

Repeat the Login process on this 2 nd page and you will be redirected to the HINARI Contents page.

Remember - If you fail to use the Login page, you will have a second option on the Content sub-page.

Once you are logged in to the HINARI Content page, access PubMed by clicking on Search inside HINARI full-text using PubMed.

Remember to access PubMed through HINARI or you will not have access to the full-text articles.

The bottom part of the initial PubMed page that is displayed here contains hypertext links to numerous databases and tools produced by the U.S. National Center for Biotechnology Information (NCBI).

Note the Bookshelf option that gives you access to numerous full text

e

-books.

The NCBI Bookshelf contains access to over 700 e-books in life science and healthcare including books, collections, databases, documentations and reports . Note the lists of New & Updated and Featured Titles . We will open the Browse Titles option.

The NCBI Bookshelf can be searched by Types, Subjects and Publishers. We have displayed the complete title alphabetical listing - with the Type of material listed in the last column. You also can complete a keyword Search.

The Search box on PubMed is active. Place your search statement in the box.

In this example, we will enter a search for

malaria infections AND africa

into the Search or query box. To execute the query, click on the Search button.

Results of the search are displayed in the main body of the page in

Summary

Format

, 20

Items per Page and

Recently Added

Sort by options . This is the default setting when you complete a search.

Note the two additional filters for Free Full Text and HINARI articles. These have been created in the HINARI/PubMed searches saved in My NCBI (see module 4.5).

Of the 4849 articles, 2159 and 2115 with Free full text are available via the HINARI filter filter ( there are some overlaps).

Note the useful options in the right column of the PubMed search results: Sort by Relevance (new October 2013) option Results by year graph Titles with your search terms listing Free full-text articles in PubMed Central (a U.S. National Institute of Health repository) Search details that include all fields (keyword) AND MeSH (Medical Subject Headings) Terms . (below those displayed)

Note the additional hypertext link for Free article . By clicking on this link, you will be re-directed to the Abstract display and be able to access the full text.

Also note the bolded terms of the search – malaria, infections and Africa and the Search details box.

If you click on the Free Article or Free PMC Article hyperlinks, you are re-directed to the Abstract display.

Click on the Full text for publication link to the publisher’s website and the full text article.

You now have access to the full text article from the Journal of Infection in Developing Countries .

We now will set the Display Settings drop down menu for the

Abstract

Format

, 20

Items per Page and

Recently Added

Sort by options. To activate these options, you will click on the Apply box.

Note the

Abstract

Format with

20

Items per page and the Recently Added Sort by options are displayed in the Display Settings line above the abstract .

Note the Free Full Text and HINARI Filters. We now will click on the HINARI one.

After clicking on the HINARI or Publisher’s icon in the Abstract display , a list of all the HINARI articles appears with the HINARI icon . By clicking on this icon or the publisher’s icon, the full-text article will display. The Free Full Text filter will work in the same way.

Note that some articles will have both the HINARI and Free Full Text icons in the Abstract display.

We have accessed the full-text article using the HINARI icon from the Abstract display. Note that you can download the article as a PDF or XML file or print the document.

Remember, you must be properly signed into HINARI to get access to the full-text articles.

In August 2010, PubMed enhanced the Abstract display . For ‘structured abstracts’, the key headings ( INTRODUCTION, RESULTS, CONCLUSIONS and KEYWORDS ) are listed at the beginning of each paragraph. Approximately 25% of the citations in PubMed use this format.

At the bottom of each citation, there is the Related citations option. The results of this search is 100 articles with 45 Free Full Text and 79 HINARI articles.

We now view the Display Settings drop down menu for the

Medline Format, 20

Items per Page and

Recently Added

Sort by options . To display click on the Apply box.

Note the listing of Medical Subject Headings (MeSH) terms in the

Medline

option . These MeSH terms are assigned by the National Library of Medicine for the indexing in PubMed. The terms can be used to make searches broader or more precise.

We now view the Display Settings drop down menu for the

Summary

Format,

200

Items per Page and

Relevance

Sort by options . To activate, click on the Apply box.

Note: The relevance sort order is based on an algorithm that analyzes each PubMed citation. For each search query, "weight" is calculated depending on how many search terms are found and in which fields they are found plus a higher weight for recently-published articles.

The larger listing of

200

Citations is useful in low-bandwidth situations. These

Summaries

are

Sorted by Relevance

.

We now view the Display Settings drop down menu for the

Summary

Format,

20

Items per Page and Sort by

Title

options .

By using the Sorted by

Title

option, this list of citations begins with National Institute of Health book chapters and then the articles are listed by title.

Another option for accessing the full-text article is to use the PubMed ID # . In HINARI/PubMed, enter the ID number in the search box. The abstract version will be displayed. If this article is a free full text or HINARI article, the icon/link will be in the top right corner of the page.

From the Send To drop down menu, we will be able to select the File, Collections, Order, Clipboard, E-mail and other options .

You must place check marks in the boxes to the left of the citations that you wish to send to File, Collections, Order, Clipboard and E-mail options.

If you do not place check marks in the boxes, the entire search will be sent to the option you choose.

From the Send To drop down menu, we will click on

File

, with the

Abstract

and

Recently Added

options . This will be a document to be downloaded from your Search.

Note how PubMed lists the # of citations you have checked.

The pubmed_results has displayed as a .txt file at the bottom of this web browser.

We will use Notepad to display the file. Note: This file is displayed in Google Chrome. In other web browsers, this will display in different places.

We now view the text from a downloaded .txt file in Notepad . You can save this file to the C:/ drive or a flash drive or a CD-Rom. Once saved, you can print the document.

Note: these are the citations of the articles. Go to the HINARI Journals Collection list to access the full-text documents.

From the Send To drop down menu, we have selected to

E-mail

with the

Summary

and a file,

Recently added

options . This will be a document to be sent to the e-mail address you entered as the recipient.

In the above message, PubMed has noted that an E-mail has been sent to the e-mail address you entered as the recipient .

From the Send To drop down menu, we have selected to send a citations to the

Clipboard

option . Note that

5

00 will be sent to the

Clipboard

since we did not check any specific articles’ boxes.

`

A green message that

500 Item were added to the Clipboard

is displayed.

Also note the number of items that have been sent to the Clipboard

.

To remove items from the Clipboard, click on

Clipboard

. The PubMed search will re-appear and, using the green hypertext links, you can

Remove all items

or

Remove from clipboard

individual citations. In this case, we will

Remove all items .

The green check box/ message notes that 500 items were deleted from the Clipboard .

One other feature of PubMed is the Single Citation Matcher . This is a useful tool if you know the author or title of the article(s) that you want.

In the Single Citation Matcher, we have entered hinari in the Title words box and clicked on Search .

Using these search terms in the Single Citation Matcher has resulted in 8 citation .

Returning to the initial PubMed page, we briefly will discuss the various training resources listed in the Using PubMed box. Note that the resources range from a Quick Start Guide to FAQs and numerous PubMed Tutorials . Remember that these resources are for general PubMed, not PubMed/HINARI.

We have accessed the PubMed Online Training page. There is a link to an extensive PubMed Tutorial and numerous Quick (animated) Tours on Searching PubMed, Managing Results, MeSH and MY NCBI plus Hot Topics .

From the initial PubMed page we have opened the PubMed New and Noteworthy page. This is the location for recent enhancements to PubMed and MY NCBI that often result in updates to the HINARI/PubMed training material.

Also available are Non-English Guides to PubMed from the National Network of Libraries of Medicine. As of July 203, these are available in 8 languages.