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

2. 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.

3. Table of Contents  Connecting to PubMed  Navigating through PubMed  Selecting a database to search on the black database bar  Searching PubMed  Query Translation  Display options  Printing, saving and email options

4. Logging on to HINARI 1 Before logging into PubMed, we can Login to the HINARI website using the URL http://www.who.int/hinari/

5. Logging into HINARI 2 We will need to insert our HINARI User Name and Password in the Login box and click on the Login button. Note: If you do not properly sign on, you will not have access to full text articles from the HINARI/PubMed database.

6. Main HINARI webpage Once you are logged in from the main HINARI webpage, access PubMed by clicking on Search HINARI journal articles through PubMed (Medline).

7. PubMed home page 1 Welcome to the PubMed Homepage. Part 1 of the tutorial will look at the interface, display options, downloading and emailing results.

8. Other NCBI databases The black bar above the query box contains links to the other NCBI databases. Highlighted above are the links to PROTEIN, OMIM, and the PubMed Journals database. To move between databases click on the database name.

9. NCBI – OMIM database Here is the OMIM database. To return to PubMed, click on the link on the database bar.

10. PubMed home page 2 Down the left-hand side of the PubMed homepage there are links to other PubMed resources including: Overview to PubMed, Help & Frequently Asked Questions, Tutorials and News items. Down the left-hand side of the PubMed homepage there are also links to other PubMed Services including: Journals Database, MeSH Database, Clinical Queries, LinkOut and Citation functions.

11. PubMed home page 3 The Search box on PubMed is active. Type here to enter your search statement.

12. PubMed search box In this example we will enter a search for malaria infections in Africa into the Search or query box. To execute the query, click on the Go button.

13. Results - default display Results of the search are displayed in the main body of the page. Note the two additional tabs for Free full text and HINARI articles (available since 07 2007). These are MyNCBI searches that are included in all the HINARI/PubMed queries (see module 4.5). Of the 1854 articles, 687 are available via the HINARI tab and 330 with Free full text tab ( there is some overlap).

14. The Details link To see how PubMed performed the search we can click on the Details link highlighted below the query box.

15. Details page PubMed uses automatic term mapping. Details shows how the PubMed software breaks down the search statement. In this example PubMed searches for Malaria as a text word and a MeSH term because of the automatic term mapping. Africa and Infections are also searched as a text words and MeSH terms.

16. Results – display options Below the query box are the default display options. Records are displayed in Summary format, records 1-20 out of 1854 are displayed and the Sort order is by PubMed ID number

17. Display formats There are a number of different formats available to display results. From the dropdown menu we can see the possible choices. When using PubMed we will use either Summary, Brief, Abstract, Citation, or Medline. The other formats are for different NCBI databases. We have selected Summary from the available options. To change the Display, click on one of the options in the dropdown menu.

18. Summary format The Summary format displays the authors names, the title of the article, the title of the source publication with citation details, and the PubMed ID number.

19. Brief format From the dropdown menu, we now will select the Brief Display option.

20. Brief format 2 The Brief Display shows the name of the first author, part of the article title, and the PubMed ID number.

21. Abstract format 1 The Abstract option is now highlighted.

22. Abstract format – full text links The Abstract Display option will show any links to publishers websites which may have the full text available. In this example we have a link to Elsevier and next to this is the HINARI icon which identifies access rights for HINARI registered institutions.

23. Abstract format – Affiliation information The Abstract Display also gives affiliation information. This affiliation information is for the first author listed on the paper, NOT all authors.

24. AbstractPlus Example This is an example of the AbstractPlus Display. Note the relocation of the HINARI and Elsevier icons.

25. Citation format 1 The Citation Display option is similar to the abstract display but has some extra information such as MeSH terms and substances included.

26. Citation format – MeSH information Here we can see the MeSH Terms assigned to the record during indexing by the National Library of Medicine (NLM).

27. MEDLINE format 1 The MEDLINE Display option is selected here.

28. MEDLINE field identifiers The MEDLINE Display option shows all the fields in the MEDLINE record with field identifiers at the beginning of each line. This format is best used for downloading records into reference managing software.

29. Number of records displayed There are a number of different options for displaying the number of references per page. These range from 5 to 500. It is advisable to download as many references per page as possible as this will save time when viewing results by eliminating the need to scroll through numerous pages. From the Show dropdown menu, 200 has been selected to re- display. To change the Show number, click on one of the options in the dropdown menu.

30. Results pages The results page is now displaying 1-200 of 1854. There are now only 10 pages of results to view.

31. Sorting options Results can be ordered alphabetically by Author or Journal title, or by publication date. In this example, Journal has been selected from the dropdown menu. To change the alphabetical order, click on one of the options in the dropdown menu.

32. Sorting by journal title The results 1-200 are now displayed alphabetically by journal title.

33. Selecting references To select references from the results list, we need to check the box on the left-hand side near the top of each record.

34. Selecting references 2 From the results page, records 1-4 now have been selected.

35. Send to Text option 1 The results selected can now be formatted for print by selecting Send to Text from the dropdown menu.

36. Send to Text option 2 This option presents a printer friendly format for output to a printer.

37. Send to File 1 To download selected results to a hard drive, floppy disk, compact disk or flash drive, select Send to File from the dropdown menu.

38. Send to File 2 Open the file in Notepad and give it a.txt file extension. Click on Save File.

39. Send to Email 1 To email selected results choose Send to E-mail from the dropdown menu.

40. Send to Email 2 From this screen, we can choose a format and sorting order, and add text notes.

41. Send to Email 3 Type in an email address in the box provided.

42. Send to Email 4 Then click on the Mail button.

43. Send to Email 5 When you return to the main results screen, a message bar appears to inform that an email has been sent from the PubMed server to the client address.

44. Send to Clipboard 1 Selected results can also be sent to a clipboard area. Select Send to Clipboard from the dropdown menu.

45. Send to Clipboard 2 An information bar will appear telling you how many results have been sent to Clipboard, the time limit after which they will be lost, and the maximum number of items allowed on the clipboard. Since we used the HINARI tab and checked five items, these have been transferred to the Clipboard.

46. Send to Clipboard 3 To retrieve items from Clipboard, click on the link below the query box.

47. Send to Clipboard 4 From within Clipboard, you can re-format and display results in the same way as you can from the main results page. Here, we have the Abstract display.

48. Send to Clipboard 5 To remove an item from Clipboard, choose Send to Clip Remove from the dropdown menu.

49. Send to Clipboard 6 An information bar will appear saying how many items were removed from the Clipboard. Note that this page uses the Summary display format.

50. This is the end of Module 4 Part 1 This is the end of Module 4 Part 1. There is a workbook to accompany this part of the module. The workbook will take you through a live session covering the topics included in this demonstration with working examples. Updated 01 2009