PubMed Database Interface Part A (Basic Course Module 4) 01 March 2018

Table of Contents Connecting to PubMed Navigating through PubMed Searching PubMed Display options Send to options All the HINARI/PubMed modules will emphasize skills on how to use PubMed as a tool to identify and access full-text articles. PubMed is the foremost biomedical database that indexes articles from 5,500+ biomedical journals. The skills in these modules include an overview of the PubMed website, using Filters 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 inside HINARI full-text using PubMed’ or you will not have access to the full-text articles. 01 March 2018

PubMed vs. Summon PubMed uses a controlled vocabulary – a human assigns medical subject headings (MeSH) to each journal article. Search results will be accurate. Summon uses the keywords in a search as it does not have a controlled vocabulary. The results are broader and you have to ‘filter’ them. The search results include journal articles and ebooks links to what is available in your country. 01 March 2018

Before logging into the PubMed, websites, we will Login to the HINARI site using the URL http://www.who.int/hinari/ 01 March 2018

Enter your HINARI USER NAME and PASSWORD in the appropriate boxes, change the language of the portal (if necessary), then click on the Login button. Note: To have access to the full text articles, you must properly sign in. 01 March 2018

Click on the Hinari logo to open the program. All the Research4Life programs are listed. Use any of the other programs by returning to this page (use the R4L Portal – Applications tab at the top of the web browser). To open another program, click on the specific logo. Your Hinari username and password will grant access to the other programs (and ditto for your institution’s AGORA, ARDI, GOALI or OARE logins). 06 March 2018

Note: The PubMed training modules use screen captures from a computer. Once logged in to the HINARI Content page, access PubMed by clicking on Databases for discovery list. In the HINARI Portal you can access PubMed from the Content page. Click on Search inside HINARI full-text using PubMed. Note: The PubMed training modules use screen captures from a computer. 01 March 2018

Open PubMed which is at the top of the Browse databases list. 01 March 2018

The Search box on PubMed is active The Search box on PubMed is active. Place your search statement in the box. In this example, enter a search for malaria infections AND africa into the Search or query box. To execute the query, click on the Search button. 01 March 2018

Results of the search are displayed in the main body of the page in Summary Format and Sort by Most Recent options. This is the default setting when you complete a search. Note that the search displays 20 per page citation. Note the two additional filters for Free Full Text and HINARI articles. These have been created for the HINARI/PubMed searches. Of the 6630 articles, 2163 are available via the HINARI filter and 3337 with Free full text filter (there are some overlaps). Some individuals prefer to view the search results with the mix of HINARI and free-full text articles while other prefer using the filters. 01 March 2018

See next slide for Find Related Data and Search details box. Note the useful options in the right column of the PubMed search results: Results by year graph PMC Images listing Find Related Data See next slide for Find Related Data and Search details box. Depending on your individual preference, some of the options in the right column will be useful to you. 01 March 2018

Highlighted are the Find related data and 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 how the PubMed search combines keywords with the Medical Subject Headings (MeSH) that are assigned by indexers at the National Library of Medicine (USA). 01 March 2018

Note the additional hypertext link for Free Article and Free PMC 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. If you complete a search in ‘regular’ PubMed, these Free Article(s) and Free PMC Article(s) will be in your search results but not the HINARI ones. Remember that there is some overlap. 01 March 2018

Click on the Free Article or Free Full Text Article hyperlinks, you are re-directed to the Abstract Format. Click on the Full text links to the publisher’s website and the full text article. 01 March 2018

You now have access to the full text article from the PLOS one journal. 01 March 2018

Check the Abstract Format bullet from the drop down menu Check the Abstract Format bullet from the drop down menu. We have retained the Sort by Most Recent option. 01 March 2018

Note the Abstract Format with the Sort by Most Recent options are displayed in the Display Settings line above the abstract. Per the Free Full Text and HINARI Filters, using these options is up to your preference. The use of the Abstract display is stressed for two reasons – you can read the abstract to confirm if this is an article you want to read and this display format has links to the free full text and HINARI full-text articles – to be discussed in the notes of the next slide. 01 March 2018

After clicking on the Abstract Format, a list of all articles appears including the HINARI and publisher’s icons and possibly the Free Full Text icons. By clicking on the HINARI icon or the publisher’s icon, the full-text article will display. Note that some (other) abstracts will have both the HINARI and Free Full Text icons in the Abstract Format. This point is critical. The Abstract format contains the icons/links to the full text. This PubMed program is called Linkout as it links to full-text articles you are able to access – either as free full text articles or those from HINARI. Note – the Linkout program does not work 100% of the time. If the HINARI icon does not work properly, click on the link to the publisher. If neither work, you will need to return to the HINARI Content page and try to access the journal article through the Journal Collection A-Z list or Publishers’ list. ‘Access Problems and Solutions’ are discussed in the Basic Course Module 3 Appendix in a presentation with that title. 01 March 2018

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. This format is quite useful as it clearly outlines the contents of the article. 01 March 2018

At the bottom of each citation, click on the Similar articles option. This option gives you access to citations and possibly full-text of articles that are similar to the original citation. 01 March 2018

The results of this search is 101 articles with 57 Free Full Text and 39 HINARI articles. 01 March 2018

Check the bullet for the MEDLINE Format and retain the Sort by Most Recent options. 01 March 2018

Note the listing of Medical Subject Headings (MeSH) terms in the MEDLINE option. These Medical Subject Headings are assigned by reviewers at the (US) National Library of Medicine. These terms are very useful for you to complete a more precise search and obtain clusters of citations on the same subject. 01 March 2018

Using the larger listing of 200 citations is useful in low-bandwidth situations. These Abstract(s) are Sort(ed) by Most Recent. 01 March 2018