1. New England Region National Network of Libraries of Medicine June 2007 The NN/LM NER is funded by the National Library of Medicine under a contract (#N01-LM-1-3518) with the University of Massachusetts Medical School in Worcester.

2. What is PubMed? The world’s premiere biomedical bibliographic database Online access to the MEDLINE database Developed & maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM)

3. Contains citations to journal articles in these major content areas: Biomedical Sciences Nursing Dentistry Veterinary Medicine Pharmacy Allied Health Preclinical sciences

4. PubMed also contains information on: Health policy Bioinformatics Health administration Standards and practice guidelines Health-related technology Patient education materials and consumer health information

5. PubMed contains: 17+ million bibliographic citations 1950 – present 5,000+ journals published worldwide are indexed 70+ languages represented Some freely available full text documents Links to the other NCBI databases

6. Accessing PubMed on the Internet: http://pubmed.gov PubMed is freely available wherever there is internet access. No registration. No subscription. No fees. No kidding. The next slide shows the homepage of PubMed.

8. Part 1: Basic Information and Navigation Very basic searching that works Results What do those icons mean? What’s a citation? In what order are search results displayed? How can I display and sort my results? What can I do with my results?

9. Type ‘n Go searching of PubMed: Simply type a term or terms in the Search Box and click Go.

10. Note that “and” is the default connector used in PubMed. If more than one term is entered into the search box, PubMed will AND the terms together. If the term AND is typed into the search box, it must be in all CAPITAL letters. This is also true with the other connecting words allowed: OR and NOT.

11. Results = a list of citations meeting the search criteria displayed in Summary format

12. What’s in a citation? Author names. Click to access abstract. Title of the journal article Journal title abbreviation and publication information The PMID is like a Social Security number for a citation. It is a unique identifier for the citation. This tag indicates the level of processing this citation has received. This particular citation has been fully processed. This icon indicates this citation has an abstract. Clicking on the icon will bring up the abstract.

13. Icons that appear in the Summary Results: No abstract available for this citation. This citation has an abstract. There is free full-text access to this article. There is free full-text access to this article through PubMed Central (PMC), an initiative from the National Library of Medicine to encourage publishers to make their content freely available.

14. About abstracts: Some citations have them, some do not. If an abstract appeared in the print publication, there will be an abstract in PubMed. Abstract length varies: some are very short; some are quite lengthy To see the abstract, click on the author name or the icon in the Summary Format.

15. More on results. Here is a search for childhood immunization refusal

16. More about results Some article titles are in brackets. Why? Some articles have no authors listed. Why? Brackets indicate the article is published in a language other than English If no authors are listed in PubMed, it’s because no authors were listed in the print version of the article.

17. Summary format: this is the default format for displaying results in PubMed. Showing 20 items per page Number of results for this search Number of pages of results The Action Bar Number of articles within this set of results that are the publication type = Review

18. Other searches may produce many more results, still in Summary format, on many pages. Move from one page to the next by clicking on Next Or, move many pages at a time by putting a number in the box next to Page and then clicking on the Page button. The way information displays on the page may also be altered.

19. Other Display Formats are available: To change from one display option to another, simply highlight the desired forma. Different formats are useful for different reasons. The Abstract format will show the abstract (where available). The AbstractPlus format shows the abstract and the first 5 Related Articles. The Citation format will show the abstract (if available) as well as the MeSH terms used to index the citation.

20. In what order are search results displayed?

22. Results are displayed in Entrez date order The citation that: meets the search criteria And was most recently added to the database will be displayed first. It is possible to sort citations into order by publication date.

23. Sorting results Sort options: -the publication date of the article -the first named author’s last name -the last named author’s last name -the title of the journal Select the desired sort option by highlighting it.

24. When searching is complete, what can be done with the results? Citations may be printed, emailed, or saved in various ways Use the Send To options:

25. First, select citations: Click the box next to the citation Have several pages of results? That’s OK. PubMed will keep track of your selected citations as you move from page to page.

26. Now, choose the Send to option: Simply highlight the desired option

27. Send to “Printer” opens a new window that allows easy printing of the selected citations Printing citations

28. Send to “Text” strips away graphics:

29. Send to File saves the selected citations as a computer file. Choosing this option will open a dialog box on your computer asking where you’d like to save the file. Send to Clipboard places the selected citations on PubMed’s Clipboard Send to Email allows users to email citations Send to RSS allows users to set up an RSS feed for this search Send to Order allows users with Loansome Doc accounts to request copies of selected articles electronically

30. CAUTION: If you do not select specific citations when you choose a Send To option, you are selecting all the citations in a given result set Up to 500 citations  will be added to the Clipboard Up to 10,000 citations  will be saved in a computer file All the citations on a single page  will appear in text only format

31. Clipboard: Holds selected search results Select citations. Highlight Clipboard.

32. When citations are added to the Clipboard: A pink banner confirms the addition The number of each selected citation turns green

33. Clipboard holds selected search results Those citations stay on the Clipboard until: The user manually removes them –or- There are 8 hours of inactivity on that computer. Close the PubMed browser, shop for airline tickets, read the Globe online, then open PubMed again -- the Clipboard items will still be there, provided there have not been 8 hours of inactivity on that computer.

34. Accessing the Clipboard Click on the Clipboard tab under the search box

35. This is the Clipboard:

36. Once in the Clipboard, the usual Send to options are there along with two new ones: Use Clip remove to remove items from the Clipboard. Select item(s), highlight Clip remove. My NCBI Collections: Allows users who have set up an account to save selected citations for longer periods of time than the Clipboard allows.

37. Send to Email Select Format and Sorting options Add a note if desired Insert email address Click Mail

38. A word about email and PubMed The sender for emails sent from PubMed will be “Sent by PubMed.” RULE OF THUMB: send emails to yourself first and then forward them on to colleagues. That way, your name will appear as the sender.

39. Review Searching Type and Go: the simplest form of searching Changing the way information displays on the page The Action Bar: display, show, sort Selecting citations Save / print / email citations Using the Send To options

40. Part 2: The Inside Scoop More on Type ‘n Go searching Using Limits to focus a search The devil’s in the details MeSH Citations & Levels of processing Automatic Term Mapping History, Related Articles, and the Single Citation Matcher in PubMed How to learn more

41. One way to narrow a broad search is to add additional terms to the search. For example, searching for citations about smallpox vaccine? Type both words into the search box: It’s still Type ‘n Go.

42. Practice Searching In Dec. 2002, newspapers reported that indoor hot tubs may be making people sick with a respiratory ailment. What’s in PubMed about this? Your search?

44. Fall 2002, NPR reported that a physician was claiming that duct tape could get rid of warts. Can you find information in PubMed on this topic? Your PubMed search?

46. Many people find that the most common problem when using PubMed is that they get too many results Adding terms to your search can help reduce the number of citations retrieved Is there another way to reduce retrieval and focus in on the topic of interest? LimitsYes!

47. Using Limits can significantly reduce the number of items retrieved. Use it to focus a search. Some of the most popular limiters are: Language Publication Type Date of publication Free full text Access the Limits page by clicking on the Limits tab:

48. Search Builders One or more author names or journal titles may be selected here and added to your search Limits Use this to limit to free full text or full text (not free) or to restrict your retrieval to only items with abstracts. Pre-specified date ranges may be chosen or you may enter a date range of your own specification Select none, one, or several options in any of these categories to focus your search results To use this option, chose a field from the drop down menu. Any terms entered into the search box will be tagged with the appropriate field tag and PubMed will search for the specified term in the specified field only.

49. Let’s limit our previous search for “smallpox vaccine” to just items written in English And then, let’s use the Type of Article limit to restrict our retrieval to citations that are Practice Guidelines When finished making selections, simply click on Go at the top or bottom of the Limits page to re-run the search with the chosen Limits applied.

50. Search results using Limits: PubMed clearly shows which Limits have been applied.

51. It’s just as simple as that. PubMed is deceptively simple to use and yet very sophisticated. The devil’s in the details.

52. The major details: What’s the organizational structure of this database? How does PubMed search?

53. Indexing allows efficient retrieval of relevant information from a database. Indexing describes content. MeSH is the controlled vocabulary used for indexing citations in PubMed. MeSH  Medical Subject Headings

54. The Citation Format displays the MeSH terms associated with a given indexed citation

55. How can I find out if a given term is a MeSH term? Use the MeSH Database Click on the link from the blue sidebar

56. PubMed’s MeSH Database:

57. The MeSH database allows searchers to look up terms and build searches. These animated tutorials teach searchers how to use the MeSH database. They are available on the MeSH Database page. Each takes only minutes to view.

58. Types of citation status tags in PubMed: [PubMed – as supplied by publisher] [PubMed – in process] [PubMed – indexed for MEDLINE] [PubMed – OLDMEDLINE] [PubMed] [PubMed – author manuscript in PMC]

59. Why would searchers want to know the different types of citations in PubMed? Only [PubMed – indexed for MEDLINE] citations have been indexed with MeSH terms. These citations will be retrieved by doing a MeSH term search. All the other citation types have no indexing attached to them. These citations will not be found by a MeSH term search.

60. OK, so MeSH is the organizing principle behind PubMed If I don’t know MeSH, can I still get good results searching PubMed? Yes! Why?

61. Automatic Term Mapping: The 3 steps PubMed goes through every time a search is executed 1. MeSH 2. Journal Title 3. Author

62. The Details Tab Look at Details to see what PubMed did with your search terms

63. Check the DETAILS tab! PRACTICE SAFE SEARCHING

64. Search measles and the Details box shows the actual search run by PubMed :

65. Automatic Term Mapping has mapped the word to its appropriate MeSH term(s) Note that text words have also been added to the search. Why? To help retrieve those non- indexed citations mentioned earlier. If a user types in a non-MeSH term as a search term, what happens?

66. Here’s how “drooling” is mapped:

67. What’s up with this: [TIAB] =Title or Abstract Medline[sb] = the subset of all indexed citations Remember that there are citations in PubMed that are not indexed with MeSH terms. This is how PubMed works to improve retrieval from all those non-indexed citations. It is looking for the word “sialorrhea” in a title or an abstract in all those citations that do not have MeSH indexing.

68. Step 1: PubMed looks for a match with a MeSH term. If a match is found, PubMed uses that MeSH term and runs the search. If no MeSH match is found, Automatic Term Mapping moves to step 2: looking for a match with a journal title. If a match is found, PubMed uses that title and runs the search. If no match is found with journal titles, it’s on to step 3: looking for a match with author names.

69. Step 2: Searching for a journal title

70. Check the DETAILS tab! PRACTICE SAFE SEARCHING

71. Since “New England Journal of Medicine” is not a MeSH term, PubMed finds no match. So, it moves to the 2 nd step: journal titles. And there it finds a match!

72. So, citations from journals may be retrieved by typing in the name of the journal or the MEDLINE abbreviation for the journal in the search box. Find all the citations from the journal “Brain” Your search?

73. Oops. What happened?

74. Check the DETAILS tab! PRACTICE SAFE SEARCHING

75. Brain maps to the MeSH term, “brain.” PubMed didn’t even get to the 2 nd step!

76. Tell PubMed what field to search. This turns off Automatic Term Mapping

77. Now, PubMed is no longer mapping the term. It is simply searching the field it has been directed to search.

78. Step 3: Author Searching Format for author names in PubMed: Last Name Initial(s) NOTE: there is no punctuation between last name and initials

80. Now that we know about Automatic Term Mapping in PubMed, let’s see how it works with a multi-term search query Let’s look at a search for head lice shampoo:

81. Head lice shampoo is NOT a Mesh term, it’s not a journal title, and it’s not an author name. So, the term on the furthest right is chopped off and PubMed looks at the remaining words as a group. Here, head lice. That maps to a MeSH term, pediculus. We can see the same format we’ve seen in previous MeSH mapping. Now, PubMed looks at the term previously cut. PubMed handles all multiple word queries like this. It looks at the whole group as a single unit. If it can’t map it, it chops from the right and looks at the remaining words. And so it goes until it can either map or it runs out of words. Shampoo is not a MeSH term, a journal title, or an author name. So, PubMed looks for this term in all fields.

82. A note on Phrases: PubMed does NOT do any proximity searching or adjacency searching Using quotation marks will force PubMed to check its phrase table, but if the phrase does not appear on that phrase table, Automatic Term Mapping will be applied. It is recommended that terms be searched with no quotation marks first.

83. Truncation The asterisk * is the truncation symbol Only end-of-word truncation is allowed in PubMed Cardio* is allowed Col*r is not allowed *megaly is not allowed Truncation turns off Automatic Term Mapping

84. Using truncation, search for all the variations of the term handwash

85. Check the DETAILS tab! PRACTICE SAFE SEARCHING

87. Sometimes, a truncated search will prompt a cautionary message in PubMed:

88. Additional details: Boolean searching is allowed: AND, OR, NOT + or – signs not allowed Combining words MUST be in all CAPITAL letters Nesting – using parentheses – is allowed. PubMed processes searches from left to right unless ( ) are used.

89. So, we’ve talked a bit about the major details: What’s the organizational structure of this database? How does PubMed search? What else is there?

90. Searches may be constructed using the: Search box: Type and Go. Highly recommended. MeSH database: see animated tutorials on the MeSH database page. History function

91. History Keeps a record of searches performed Rerun searches Delete searches View the Details for a selected search Combine previous searches to make new searches Access History by clicking on the History tab under the search screen

93. History remains until there are 8 hours of inactivity or until the searches are manually deleted from History. The Clear History button will delete everything in History.

94. Each of the query numbers is hyperlinked. Click on the query number and a menu will appear:

95. Combine searches using AND, OR, or NOT Erase this specific search from History using Delete Return to this search using Go See the Details tab for this search using Details This search can be saved in My NCBI

96. To find information about smallpox and bioterrorism Click on the search number for smallpox, highlight AND Click on the search number for bioterrorism, highlight AND Click Go at the right side of the search box to run the search.

97. Some final thoughts on searching PubMed: Related Articles Single Citation Matcher My NCBI

98. Related Articles: Articles similar to the one you are viewing are displayed automatically in AbstractPlus format:

99. Related Articles may also be retrieved via the Related Articles link on the Summary format: Find one article you like, click Related Articles and PubMed will do a search for similar articles. Read about the algorithm for this related articles search in PubMed’s Help

100. The Single Citation Matcher in PubMed From the blue sidebar, click here Fill in one or more boxes and PubMed will search for citations that meet your specifications.

101. My NCBI This free service allows users to set up accounts and: Customize their searching Save search strategies and have PubMed automatically email them updated results Save search results indefinitely Turn on highlighting of search terms And more…

102. Learn more about My NCBI From the blue side bar in PubMed, click on Tutorials. Several “Quick Tours” are available for My NCBI From the NER website, see the “Using My NCBI” presentation

103. Other capabilities of PubMed Journals Database Clinical Queries Special Queries LinkOut

104. So, you want to learn more? Overview Tutorial Help & FAQ New/Noteworthy

105. Animated tutorials are on how to use the MeSH database and how to construct author and subject searches are available on this NLM website: http://www.nlm.nih.gov/bsd/dist_edu.html There is a PubMed manual available on the web: http://www.nlm.nih.gov/pubs/web_based.html Contact your regional medical library for information on free training: http://nnlm.gov

106. Hmmm….. Better write a note to myself to check the Details tab in PubMed