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

2. http://www.MCST-IS- CS.wikispaces.com

3. 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.

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

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

6. Logging into HINARI 2 You need to enter your HINARI User Name and Password in the appropriate boxes, then click on the Login button. Note: If you do not properly sign on, you do not have access to full text articles.

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

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

9. In October 2009, the PubMed display was re- designed in a simpler and more intuitive fashion. Remember to access PubMed through HINARI or you will not have access to the full-text articles.

10. 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.

11. 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.

12. 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. If you click on Book Types, you can access 110 ‘books’.

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

14. 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 4237 articles, 2030 are available via the HINARI filter and 1717 with Free full text filter ( there are some overlaps).

15. Note the useful options in the right column of the PubMed search results: 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.

16. 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 how the terms of the search – malaria, infections and Africa - are bolded if found in the title.

17. From the Abstract display, click on the hypertext link to the publisher’s website and the full text article. For HINARI articles, there will be HINARI icons and links.

18. You now have access to the full text article from the Malaria Journal.

19. 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.

20. 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.

21. After clicking on the HINARI filter in the Abstract display, a list of all the HINARI articles appears with the HINARI icon. By clicking on this 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.

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

23. 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.

24. At the bottom of each citation in Abstract format, information about the Publication Types, MeSH Terms and Grant Support can be displayed. Click on the drop down menu to view this information.

25. 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.

26. 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.

27. We now view the Display Settings drop down menu for the Summary Format, 200 Items per Page and Recently Added Sort by options. To activate, click on the Apply box.

28. The larger listing of citations is useful in low-bandwidth situations.

29. We now view the Display Settings drop down menu for the Abstract Format, 50 Items per Page and Sort by Title options.

30. By using the Sort by Title option, this list of citations begins with A.

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

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

33. From the Send To drop down menu, we will click on Create File, with the Abstract and Recently Added options. This will be a document to be downloaded from your Web Browser.

34. 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.

35. 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.

36. From the Send To drop down menu, we have selected to E-mail a file, with the Summary and Recently added options. This will be a document to be sent to the e-mail address you entered as the recipient.

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

38. From the Send To drop down menu, we have selected to send a citations to the Clipboard option. Note that 5 checked items will be sent to the Clipboard.

39. In case, we have not checked the boxes in any of the citations, the first 500 items will be added to the Clipboard.

40. The green message confirms that 500 items have be added to the Clipboard. Note that the Clipboard items will be lost after 8 hours.

41. ` In the Display Settings, a green check Item in clipboard message is noted for all the items you have selected. Also note the number of records that has been sent to the Clipboard.

42. 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.

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

44. 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.

45. In the Single Citation Matcher, we have entered aronson b in the Author name box and hinari in the Title words box. We will click on the Go box.

46. Using these search terms in the Single Citation Matcher has resulted in 1 citation.

47. We have repeated this search but only for the author aronson b and excluded HINARI in the Title words box. The result of this broader search is 70. Note that there appear to be at least 3 articles by this author about HINARI or related issues.

48. As of April 2010, PubMed has added links to Free PubMed Central articles and Books & Documents from the NCBI Bookshelf. Besides Free Article hyperlinks, you will see Free text links to PMC articles and Books & Documents.

49. 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.

50. 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.

51. This is the end of Module 4 Part 1. There is a workbook to accompany this part of the module. It will take you through a live session covering the topics included in this demonstration with working examples. Updated 2013 04 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.