PubMed Database Interface (Basic Course Module 4 Part A) 05 July 2017

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. 05 July 2017

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. 05 July 2017

Before logging into the PubMed, websites, we will Login to the HINARI site using the URL http://www.who.int/hinari/ 05 July 2017

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. 04 July 2017

Click on the Hinari logo to open the program. All the programs your institution is registered for are listed. Login to 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 or OARE logins). 04 July 2017

Access to Full-text articles from SAML Publishers Elsevier, Oxford University Press, Springer, Thieme and Wolters Kluwer – Lippincott, Williams & Wilkins use the SAML authentication system. For access to full-text articles via Hinari/PubMed, (Hinari/Summon and Google Scholar), a journal from these publishers needs to be opened in Hinari prior to opening the specific programs. Go to the Hinari Training page (www.who.int/hinari/training/ ), open Hinari_Basic_Course_Module_4_Appendix and follow the instructions. 05 July 2017

Once you are logged in to the HINARI Content page, access PubMed by clicking on Search inside HINARI full-text using PubMed. In the HINARI Portal you can access PubMed from the Content page. Click on Search inside HINARI full-text using PubMed. 05 July 2017

HINARI PubMed – Access to Full Text (July 2017) HINARI LOGIN PubMed Login LINKOUT LINK FULL TEXT ALTERNATIVE Login to HINARI Search inside HINARI full-text using PubMed Click on LINKOUT link to obtain Full Text. To use PubMed MyNCBI – do not login to HINARI. (save searches, create collections, custom filters) Login directly at PubMed: www.ncbi.nlm.nih.gov/pubmed/ LINKOUT (access to HINARI full-text articles) will not work. To access HINARI full-text articles, go to the HINARI content page Journals collection A-Z list. 05 July 2017

Remember to access PubMed through HINARI or you will not have access to the full-text articles. Note – you can open PubMed directly but, by not accessing from HINARI, you will not have the links to the HINARI full-text articles that the publishers have granted access to your institution. You only will have access to free-full text articles. 05 July 2017

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. 05 July 2017

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 6163 articles, 3282 are available via the HINARI filter and 2520 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. 05 July 2017

Titles with your search terms listing Find Related Data Note the useful options in the right column of the PubMed search results: Results by year graph Titles with your search terms listing Find Related Data See next slide for Search details box. Depending on your individual preference, some of the options in the right column will be useful to you. 05 July 2017

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 how the PubMed search combines keywords with the Medical Subject Headings (MeSH) that are assigned by indexers at the National Library of Medicine (USA). 05 July 2017

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. 05 July 2017

If you click on the Free Article or Free PMC 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. 05 July 2017

You now have access to the full text article from the BioMed Central journal. 05 July 2017

We now will check the Abstract Format bullet from the drop down menu We now will check the Abstract Format bullet from the drop down menu. We have retained the Sort by Most Recent option. 05 July 2017

Note the Abstract Format with the Sort by Most Recent options are displayed in the Display Settings line above the abstract. Note 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. 05 July 2017

After clicking on the Abstract Format, a list of all articles appears including the HINARI and publisher’s icons and/or Free Full Text icons. By clicking on the HINARI icon or the publisher’s icon, the full-text article will display. Note that some articles 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. 05 July 2017

Use of PubMed ‘LinkOut’ – direct access to Hinari publishers’ full-text articles In the ‘Abstract’ display, there will be icons/links to the full-text articles (PubMed’s LinkOut option). This option IS NOT completely reliable. Sometimes, one of the icons/links works while the others do not (HINARI vs. a specific publisher vs. PMC). Instead of getting access to the html or pdf of the article, you are asked to ‘pay’ or ‘login’ and the HINARI password will not work. Note: LinkOut does not know if the publisher has or has not granted access to your institution. 1st, try all the icons/links. 2nd, if none of the icons/links work, return to the HINARI content page Journals collection A-Z list or specific Publishers list and open the journal title and volume/issue for access to the full-text article. A green box means that you will have access to the journal. 05 July 2017

Open the .txt file. Copy the article title. A second option when the ‘Linkout’ software does not access the full text articles is to use the Hinari Summon search tool. In PubMed, check the boxes of the articles you want. Save the articles to a file (use the send to drop down menu). Open the .txt file. Copy the article title. Open Summon (bottom of Search inside Hinari fulltext through database… list) In Summon, enter the title in the Search box and complete search. Note: if your institution does not have access to the specific publisher, you will not get the full-text of this article in Summon. For more info on Summon, go to Hinari Basic Course Module 7. 05 July 2017

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 20% of the citations in PubMed use this format. This format is quite useful as it clearly outlines the contents of the article. 05 July 2017

This option gives you access to citations and possibly full-text of articles that are similar to the original citation. At the bottom of each citation, there is the Similar articles option. The results of this search is 101 articles with 56 Free Full Text and 38 HINARI articles. 05 July 2017

The results of this search is 99 articles with 44 Free Full Text and 37 HINARI articles. 05 July 2017

We now will check the bullet for the MEDLINE Format and retain the Sort by Most Recent options. 05 July 2017

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. 05 July 2017

We now will check the bullet for the 200 Items per page. 05 July 2017

The larger listing of 200 citations is useful in low-bandwidth situations. These Abstract(s) are Sort(ed) by Most Recent. 05 July 2017

We now will open the Best Match Sort by option from the drop down menu with the Abstract option. Note: The ‘Best Match’ 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. Some individuals prefer this option which is similar to the relevance ranking of Google, Scholar and other search engines. Since this option is based on the MeSH controlled vocabulary, the results are significantly more precise than the keyword search of Google or Scholar. 05 July 2017