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  • How many of you have gone shopping online? Whether you’ve realized it or not, when you’ve gone online shopping you’ve actually used a database.
  • Some databases only contain information about journal, or scholarly, literature – depends on database.
  • Citation gives information needed to locate the article.
  • Assigning of subject headings takes time.
  • Handout

    1. 1. Introduction to MEDLINE/PubMed CDENT 5141: Dental Informatics Spring 2009 John Siegel, MLS, Reference Librarian Liaison to the School of Dental Medicine
    2. 2. Game On! “The Price is Right” <ul><li>Two contestants….if I call your raffle ticket number, come on down! </li></ul><ul><li>“ Name That Price” </li></ul><ul><li>Guess the correct price and win a prize! </li></ul><ul><li>Each contestant will have the opportunity to take away up to two incorrect prices by answering two questions correctly. </li></ul>
    3. 3. “ Name That Price!” <ul><li>According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by a general dentist? </li></ul><ul><li>$250 </li></ul><ul><li>$300 </li></ul><ul><li>$400 </li></ul><ul><li>$500 </li></ul>
    4. 4. “ Name That Price!” Elimination Question #1 <ul><li>What is a citation? </li></ul><ul><li>a. Information required to identify a particular </li></ul><ul><li>library, such as a university or public </li></ul><ul><li>b. Information required to identify a particular </li></ul><ul><li> resource, such as a book or journal </li></ul><ul><li>c. Good question! </li></ul><ul><li>d. None of the above. </li></ul>
    5. 5. “ Name That Price!” Elimination Question #2 <ul><li>What information is included in a citation for </li></ul><ul><li>a journal article ? </li></ul><ul><li>a. Authors </li></ul><ul><li>b. Title of Article </li></ul><ul><li>c. Title of Journal </li></ul><ul><li>d. All of the above </li></ul>
    6. 6. “ Name That Price!” <ul><li>According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by a general dentist? </li></ul><ul><li>Correct Answer: $300 </li></ul>
    7. 7. “ Name That Price!” <ul><li>According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by an oral and maxillofacial surgeon (not including x-rays or anesthesia)? </li></ul><ul><li>$400 </li></ul><ul><li>$450 </li></ul><ul><li>$500 </li></ul><ul><li>$600 </li></ul>
    8. 8. “ Name That Price!” Elimination Question #3 <ul><li>In addition to or besides the title, how can you distinguish a scholarly journal from a magazine? </li></ul><ul><li>a. A scholarly journal does not include articles on current topics. </li></ul><ul><li>b. A scholarly journal generally has a panel of subject experts review the articles. </li></ul><ul><li>c. A scholarly journal has more interesting articles than a magazine. </li></ul><ul><li>d. None of the above. </li></ul>
    9. 9. “ Name That Price!” Elimination Question #4 <ul><li>Which of the following is true about a </li></ul><ul><li>journal article abstract? </li></ul><ul><li>a. It includes a reference list for the reader. </li></ul><ul><li>b. It is usually several pages long. </li></ul><ul><li>c. It summarizes the article for the reader. </li></ul><ul><li>d. None of the above </li></ul>
    10. 10. “ Name That Price!” <ul><li>According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by an oral and maxillofacial surgeon (not including x-rays or anesthesia)? </li></ul><ul><li>Correct Answer: $500 </li></ul>
    11. 11. Friedman Article Citation <ul><li>Friedman, J. W. (2007). The prophylactic extraction of third molars: A public health hazard. American Journal of Public Health, 97 (9), 1554-1559. </li></ul>
    12. 12. “ Bonus Question” <ul><li>You are performing a routine examination on one of patients, who is 17 years old. You determine from x-rays that his wisdom teeth are impacted. </li></ul><ul><li>You ask the patient if he is having any symptoms, such as pain, and he says no. </li></ul>
    13. 13. “ Bonus Question” <ul><li>Knowing that it is a commonly accepted and performed procedure, yet given possible complications (i.e. pain, time missed from work/school) and cost, would you recommend extraction of this patient’s wisdom teeth? </li></ul><ul><li>Why or why not? </li></ul><ul><li>How would you decide? </li></ul>
    14. 14. Common “Ways of Knowing” <ul><li>Ask a colleague </li></ul><ul><li>Legacy – always done it this way </li></ul><ul><li>Internet resources </li></ul><ul><li>Textbooks, other books </li></ul><ul><li>Professional meeting papers/presentations </li></ul><ul><li>Journal literature – scientific studies </li></ul>
    15. 15. Evidence-Based Dentistry <ul><li>“ An approach to oral health care that requires the judicious integration of systematic assessments of clinically relevant scientific evidence , relating to the patient's oral and medical condition and history, with the dentist's clinical expertise and the patient's treatment needs and preferences.” </li></ul><ul><li>Source: American Dental Association. (2008). Evidence Based Dentistry: Glossary of Terms. Retrieved February 27, 2008, from http://www.ada.org/prof/resources/ebd/glossary.asp . </li></ul>
    16. 16. Evidence-Based Dentistry Clinician’s Clinical Expertise Patient’s Needs and Preferences Assessment of Scientific Literature
    17. 17. Database <ul><li>Organized </li></ul><ul><li>Searchable </li></ul><ul><li>Contains information about something specific (individual iTune songs, pictures of Chicago, etc.) </li></ul><ul><li>It doesn’t have to be, but often electronic </li></ul>
    18. 18. Bibliographic Databases at the Library Information about Joseph (Joe) Schmoe’s accepted journal article Information about Junior’s accepted journal article Information about other journal articles, and sometimes magazines, newspapers Bibliographic Database
    19. 19. Bibliographic Databases: What information are we talking here? <ul><li>Author </li></ul><ul><li>Date article was published </li></ul><ul><li>Title of article </li></ul><ul><li>Title of journal, magazine, or newspaper that article appeared in </li></ul><ul><li>Volume, Issue </li></ul><ul><li>Page numbers </li></ul>ARTICLE CITATION
    20. 20. <ul><li>In addition to article citations, bibliographic databases generally also contain the following useful pieces of information: </li></ul><ul><ul><li>Abstract = Brief synopsis of article </li></ul></ul><ul><li> Think of as “Coming Attraction” </li></ul><ul><ul><li>Subject headings = Standardized vocabulary </li></ul></ul><ul><ul><li> “ You say tomato, I say to-ma-to” </li></ul></ul>Bibliographic Databases: What information are we talking here?
    21. 21. MEDLINE <ul><li>Electronic bibliographic database maintained by the National Library of Medicine </li></ul><ul><li>Contains citations (not-full text) to biomedical literature (including dentistry) </li></ul><ul><li>Citations date back to 1950s </li></ul><ul><li>Most newer citations include abstracts </li></ul><ul><li>All citations include subject headings : Medical Subject Headings (MeSH) </li></ul>
    22. 22. Subject Headings: You Say Tomato, I Say To-ma-to <ul><li>Article A </li></ul><ul><li>Title: </li></ul><ul><li>Wisdom tooth extraction. </li></ul><ul><li>Article B </li></ul><ul><li>Title: </li></ul><ul><li>Third molar extraction. </li></ul>Medical Subject Heading (MeSH) for both titles: Molar, Third
    23. 23. PubMed: MEDLINE and More <ul><li>National Library of Medicine’s interface to access MEDLINE </li></ul><ul><li>PubMed also allows you to search citations that have not been assigned controlled vocabulary (MeSH) – Generally newest citations </li></ul>
    24. 24. Accessing PubMed <ul><li>Two ways to access PubMed </li></ul><ul><ul><li>Freely: www.pubmed.gov </li></ul></ul><ul><ul><li>Through your university health sciences library </li></ul></ul><ul><li>It is recommended that you access PubMed through your university health sciences library to take advantage of full-text links </li></ul>
    25. 25. Searching PubMed <ul><li>Notice “Search Box” (similar to Google) </li></ul><ul><li>Best not to overload search box: Use a few selective keywords </li></ul>
    26. 26. Formulating Your Search: Building Block Approach <ul><li>Refer to your research question </li></ul><ul><li>For example, let’s refer back to your patient with the asymptomatic, impacted wisdom teeth: </li></ul><ul><li>In the case of asymptomatic, impacted wisdom teeth, is extraction a viable treatment? </li></ul>
    27. 27. Formulating Your Search: Building Block Approach <ul><li>Pull out the major concepts (either single words or phrases) that will serve as keywords </li></ul><ul><li>Use the BOOLEAN operator “AND” ( must be capitalized) to combine concepts </li></ul>
    28. 28. Formulating Your Search: Building Block Approach <ul><li>In the case of asymptomatic, impacted wisdom teeth, is extraction a viable treatment? </li></ul><ul><li>What keywords would you use? </li></ul><ul><li>Keyword #1: ____________________ </li></ul><ul><li>Keyword #2: ____________________ </li></ul><ul><li>Keyword #3: ____________________ </li></ul><ul><li>Keyword #4: ____________________ </li></ul>
    29. 29. Formulating Your Search: Building Block Approach <ul><li>In the case of asymptomatic, impacted wisdom teeth, is extraction a viable treatment? </li></ul><ul><li>What keywords would you use? </li></ul><ul><li>Keyword #1: wisdom teeth </li></ul><ul><li>Keyword #2: asymptomatic </li></ul><ul><li>Keyword #3: impacted </li></ul><ul><li>Keyword #4: extraction </li></ul>
    30. 30. Formulating Your Search: Building Block Approach <ul><li>Search strategy for the previous question, with BOOLEAN operator “AND” inserted between keywords: </li></ul><ul><li>wisdom teeth AND asymptomatic AND impacted AND extraction </li></ul><ul><li>We’re using the BOOLEAN operator “AND” because we want citations to articles that contain all of these concepts </li></ul>
    31. 31. Formulating Your Search: Building Block Approach/Nesting <ul><li>You may want to consider adding synonyms for one or more concepts. </li></ul><ul><li>If you add synonyms, you must incorporate a search technique known as nesting, which uses parentheses (as shown below) </li></ul><ul><li>In addition to nesting, you must include the BOOLEAN operator “OR” (capitalized) between synonyms </li></ul>
    32. 32. Formulating Your Search: Building Block Approach/Nesting <ul><li>Example: </li></ul><ul><li>Concept #1: wisdom teeth </li></ul><ul><li>Concept #2: (asymptomatic OR prophylactic) </li></ul><ul><li>Concept #3: impacted </li></ul><ul><li>Concept #4: extraction </li></ul><ul><li>Search strategy, with nesting and BOOLEAN operator “OR” inserted between synonyms: </li></ul><ul><li>wisdom teeth AND (asymptomatic OR prophylactic) AND impacted AND extraction </li></ul>
    33. 33. Some Tips… <ul><li>Avoid quotation marks around phrases, as this turns off one part of PubMed’s search function – stay tuned! </li></ul><ul><li>Wildcard/truncation search – i.e. dental cleaning* to retrieve dental cleaning, dental cleanings – also turns off one part of PubMed’s search function – continue to stay tuned! </li></ul>
    34. 34. Search Statement Recap <ul><li>wisdom teeth AND asymptomatic AND impacted AND extraction </li></ul>
    35. 35. Running Your Search in PubMed Must say “PubMed” Enter your search statement, making sure that BOOLEAN operators (AND, OR, NOT) are CAPITALIZED, then hit “Go”
    36. 36. Examining PubMed Results To view the abstract for a particular article, click on the authors link Change the Show feature from “20” to “50” by using the small down arrow to the right.
    37. 37. Limits in PubMed <ul><li>Limits are an excellent way to target your citation retrieval </li></ul><ul><li>Example of limits you might use: </li></ul><ul><ul><li>Language: Since MEDLINE/PubMed contains citations for articles beyond English journals (global coverage), limit your search to English </li></ul></ul><ul><ul><li>Age </li></ul></ul><ul><ul><li>Type of article: Includes limits for evidence-based dentistry (i.e. meta-analysis, practice guidelines, clinical trials, randomized control trials) </li></ul></ul>
    38. 38. Applying Limits to PubMed Searches Click once on the “Limits” tab
    39. 39. Applying Limits to PubMed Searches To apply the “English” Language limit, click once in the small box to the left of “English”
    40. 40. Applying Limits to PubMed Searches Be sure to click once on the “Go” button at the bottom of the screen after you have selected your limits
    41. 41. Applying Limits to PubMed Searches If limits are applied successfully, you should see the above
    42. 42. The PubMed Record: A Closer Look To find similar articles, click on the “See all Related Articles” NOTE: DO NOT USE FOR WRITTEN ASSIGNMENT! To obtain the full title of a journal, scroll over the journal abbreviation. To find similar citations (for other research and review articles) – DO NOT USE THESE LINKS FOR YOUR ASSIGNMENT! Link to full-text
    43. 43. “ Displays” in PubMed <ul><li>PubMed has a variety of “Display” options, which affect how citations and other information appear </li></ul><ul><li>Common “Displays”: </li></ul><ul><li>Summary – default view; shows citation, </li></ul><ul><li>Abstract –Citation and abstract, link to full-text at HSLS </li></ul><ul><li>AbstractPlus – same as Abstract + related links </li></ul><ul><li>Citation – Citation, abstract, and subject headings </li></ul><ul><li>MEDLINE – Use to import citations into citation management software (i.e. EndNote, RefWorks) </li></ul>
    44. 44. Citation Output Options <ul><li>You have a variety of options for working with your citations away from PubMed: </li></ul><ul><li>Text – Allows you to copy and paste citations into another document </li></ul><ul><li>File – Allows you to save citations to a text file </li></ul><ul><li>Printer – Allows you to print citations </li></ul><ul><li>E-mail - Send selected citations </li></ul><ul><li>Collections – Set up a free MyNCBI account to save citations online for future reference </li></ul>
    45. 45. PubMed History: Record of Searches
    46. 46. Exploring Medical Subject Headings (MeSH) <ul><li>Approximately 25,000 terms </li></ul><ul><li>Human indexers assign these terms to citations, based on reading the abstract or complete article </li></ul><ul><li>Provides a controlled means of searching – a concept may be referred to in several different ways, allows standardization </li></ul><ul><li>Compare to keywords – not standardized </li></ul><ul><li>PubMed’s default is to combine keyword and MeSH searching </li></ul>
    47. 47. Exploring Medical Subject Headings (MeSH) <ul><li>Title #1: Title #2: </li></ul><ul><li>Review of the current Clinical challenges </li></ul><ul><li>status and challenges for and the relevance </li></ul><ul><li>dental posterior restorative of materials testing </li></ul><ul><li>composites : Clinical, for posterior </li></ul><ul><li>chemistry, and physical composite </li></ul><ul><li>behavior considerations restorations </li></ul><ul><li>MeSH headings for both titles: </li></ul><ul><li>Composite Resins </li></ul><ul><li>Dental Restoration, Permanent </li></ul>
    48. 48. Exploring MeSH: The MeSH Database To access MeSH database
    49. 49. Important Things to Know About the MeSH Database <ul><li>You aren’t searching PubMed when you search the MeSH database </li></ul><ul><li>The MeSH database contains records about the MeSH terms </li></ul><ul><li>These records include the following fields: </li></ul><ul><ul><li>MeSH term </li></ul></ul><ul><ul><li>Scope note (definition) – though a scope note may not always be present </li></ul></ul><ul><ul><li>Entry terms </li></ul></ul>
    50. 50. Exploring MeSH: The MeSH Database Enter each keyword individually in the search box, then hit “Go” button
    51. 51. The MeSH Database: MeSH Records – Things to Know ENTRY TERMS ARE NOT THE SAME AS MESH TERMS! “ Entry terms” are keywords/text words, which are not standardized. If you search the MeSH database for one of these “entry terms” OR your PubMed search statement includes one of these “entry terms,” PubMed automatically searches the MeSH heading. In this case, we searched for “wisdom teeth,” which PubMed “translated” and then searched as MeSH term, “Molar, Third.” Scope note: Definition of MeSH term – May not always be present MeSH term – answer(s) for question #4
    52. 52. The MeSH Database: List of Possible MeSH terms <ul><li>Generally you will not see a MeSH record “pop-up” when you enter a term, as in the previous slide. </li></ul><ul><li>You are more likely to get a list of MeSH terms and you will have to pick the term that fits your concept. </li></ul><ul><li>Again, remember that in the MeSH database, you’re only searching MeSH terms. PubMed isn’t actually doing a search. </li></ul>
    53. 53. The MeSH Database: List of Possible MeSH terms MeSH term Scope note If you don’t find a MeSH term that matches in your list, try clicking on one of the MeSH terms that appears as a “Suggestion”
    54. 54. MeSH Database Exercise <ul><li>Using the MeSH database, identify MeSH terms for the remainder of the keywords in the wisdom teeth example. [HINT: There may not be a MeSH term for one keyword] </li></ul><ul><li>Tooth Extractions ____________________ </li></ul><ul><li>Dental cleaning _______________________ </li></ul><ul><li>Sleep _______________________________ </li></ul><ul><li>Asymptomatic ________________________ </li></ul>
    55. 55. MeSH Database Exercise <ul><li>Using the MeSH database, identify MeSH terms for the remainder of the keywords in the wisdom teeth example. [HINT: There may not be a MeSH term for one keyword] </li></ul><ul><li>Tooth extractions Tooth extraction </li></ul><ul><li>Dental cleaning Dental prophylaxis </li></ul><ul><li>Sleep Sleep </li></ul><ul><li>Asymptomatic No MeSH match </li></ul>
    56. 56. MeSH Database: Final Reminders <ul><li>Remember, when you search the MeSH database you’re not searching PubMed </li></ul><ul><li>You generally will get a list of possible MeSH terms – you will need to pick-out the MeSH term that best fits your concept </li></ul><ul><li>An entry term is NOT the same as the MeSH term </li></ul><ul><li>Sometimes the keyword you type in may be the same as the MeSH term (i.e. keyword sleep = MeSH term Sleep </li></ul>
    57. 57. PubMed Behind the Scenes <ul><li>Two components of PubMed search: </li></ul><ul><li>When you do a search in PubMed, PubMed will search for the terms you enter [ keyword/text word searching] </li></ul><ul><li>AND </li></ul><ul><li>PubMed will attempt to “translate” the terms you enter into Medical Subject Headings (MeSH), then it will search any “translated”/”mapped” MeSH terms [subject searching via PubMed’s automatic term mapping feature] </li></ul>
    58. 58. Understanding How PubMed Processed Your Search Click once on the “Details” tab
    59. 59. Understanding How PubMed Processed Your Search Wherever you see the phrase “MeSH Terms” in brackets, PubMed automatically searched these MeSH terms. In this case, by “wisdom teeth” PubMed thought we were referring to the MeSH term “molar, third.” PubMed searched the MeSH term “molar, third.” Note that PubMed did not map to any other MeSH terms in this example (see “Translations” section below). Be sure to look for the “MeSH Terms” in brackets throughout the translation section. Any words in quotes in front of the “MeSH Terms” in brackets is a MeSH term that PubMed searched.
    60. 60. Single Citation Matcher: When You Have an Incomplete Citation…
    61. 61. Single Citation Matcher: When You Have an Incomplete Citation… <ul><li>Will allow you to “plug in” the information you have to find the citation </li></ul><ul><li>Type author’s names (if applicable) as Last Name<space>First Initial </li></ul><ul><li>For date, you can type a month and year or just a year – enter as YYYY/MM OR YYYY </li></ul><ul><li>Process of trial and error – If there is no citation “match,” try revising the information you typed (i.e. just enter the Author’s last name, without first initial; just enter the year, without the month) </li></ul>
    62. 62. Identifying Citation Information To obtain the full title of a journal, scroll over the journal abbreviation In this example: 204 is volume; 4 is issue (in parentheses); E7 is page number

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