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Point-Blank. 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. What is PubMed?

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  1. Point-Blank 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.

  7. 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?

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

  9. 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:ORand NOT.

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

  11. 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.

  12. Icons that appear in the Summary Results: No abstract available for this citation. 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. This citation has an abstract.

  13. 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.

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

  15. 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.

  16. The Action Bar 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 articles within this set of results that are the publication type = Review Number of pages of results

  17. 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.

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

  19. In what order are search results displayed?

  20. 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.

  21. 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.

  22. 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:

  23. 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.

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

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

  26. Send to “Text” strips away graphics:

  27. 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 Clipboardplaces the selected citations on PubMed’s Clipboard • Send to Emailallows 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

  28. 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

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

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

  31. 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.

  32. Accessing the Clipboard • Click on the Clipboard tab under the search box

  33. This is the Clipboard:

  34. 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.

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

  36. 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.

  37. 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

  38. 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

  39. 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.

  40. 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?

  41. 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?

  42. 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? Yes! Yes! Limits

  43. 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:

  44. 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.

  45. 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.

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

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