PubMed Database Interface (Basic Course: Module 4)

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 All the HINARI/PubMed modules will emphasize skills on how to use PubMed as a tool to identify full-text articles. PubMed is the foremost biomedical database that indexes articles from over 5,100+ biomedical journals. The skills in these modules include an overview of the PubMed website, using LIMITS in PubMed, Medical Subject Headings (MESH) and other tools (preview/index, filters and history) for search strategies and using ‘MY NCBI’, a platform that allows you to setup filter tabs in your display area, save searches and receive automatic email alerts to new articles added to PubMed. By learning these skills, you will master an invaluable option for utilizing the e- journals that are available via HINARI particularly since you will be able to identify articles available from multiple journals and HINARI associated publishers. Similarly to the first module, you will need access to the Internet and be required to complete a series of exercises. You must login to HINARI and then go to ‘search for articles through PubMed (Medline)’ or you will not have access to the full-text articles.

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

We will need to enter our HINARI User Name and Password in the appropriate boxes, then click on the Login button. To have access to the full text articles, you must properly sign in. Since the migration to a new authentication server (Jan. 2014), we strongly recommend use of Chrome or Mozilla. If you use Internet Explorer, you will need to login twice.

If you are using Internet Explorer, repeat the Login process on this 2nd page and you will be redirected to the HINARI Contents page.

Once you are logged in to the HINARI Content page, access PubMed by clicking on Search inside HINARI full-text using PubMed. From the HINARI Portal you can access PubMed from the “Find articles” link in the body of the webpage. Click on Search for articles through PubMed (Medline).

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

The Search box on PubMed is active 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 for the HINARI/PubMed searches. Of the 5009 articles, 2275 are available via the HINARI filter and 2128 with Free full text 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) See next slide for Search details box.

Highlighted are the Search details that include all fields (keyword) for malaria, infection, infections and africa AND MeSH (Medical Subject Headings) Terms for malaria, infection and africa. The MeSH Terms are assigned by indexers of the National Library of Medicine. For more information, go to the Advanced Course Module 1.

Note the additional hypertext link for Free article 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 Malaria Journal.

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 and publisher’s icons. By clicking on the HINARI 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 HTML or PDF 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 In August 2010, PubMed enhanced the Abstract display . For ‘structured abstracts’, the key headings (INTRODUCTION/BACKGROUND, METHODS AND FINDINGS RESULTS and/or, 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 many of the Abstract displays, you can click on the Publication Types or MeSH Terms. This option gives you other Medical Subject Headings that can be used to make searches broader or more precise. For more information, go to the Advanced Course Module 1.

At the bottom of each citation, there is the Related citations option 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.

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 lists of citations begins with A 10 year study…

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.