Introduction to PubMed for LIS students

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  • Single Citation MatcherJournals Database. This database can be used to search for journals by journal title, Medline title abbreviation, or the International Standard Serial Number (ISSN). Clinical QueriesResults of searches on this page are limited to specific clinical research areas using automatic Research Methodology Filters.
  • PubMed has a total of more than twenty 20 citations and MEDLINE contains more than 17 million.OLDMEDLINE for pre-1966 citations. (~2 million citations as of 2010) Citations out-of-scope (e.g., covering plate tectonics or astrophysics) from some journals, primarily general science and general chemistry journals, for which the life sciences articles are indexed for MEDLINE In-process citations with records for articles before indexed with MeSH, added to MEDLINE or converted to out-of-scope status Citations that precede when a journal was selected for MEDLINE indexing (when supplied electronically by the publisher) Some life science journals that submit full text to PubMed Central and may not have been recommended for inclusion in MEDLINE although they have undergone a review by NLM, and some physics journals that were part of a prototype PubMed in the early 1990s
  • Created in 1960Similar in concepts to kw on other systemsMeSH represent a medical concept as well as none-medical Can be broad or narrowCitation is enhanced by MESH
  • Search forBeverages to show the headings / subheadingsSearch for lung cancer review chemotherapy (page 10 or so) to show other things Search for EyelidEyelid is intended under eye because narrower in scope Many heading occurs in different branches
  • http://www.nlm.nih.gov/bsd/disted/video/How to search only with MeSH (try beverages) - look at the handoutTalk about entry termsExplode and majorHow powerful is mapping?Type beveragesNow type beverage*
  • http://www.nlm.nih.gov/bsd/viewlet/search/subject/subject.html
  • What characterizes a good question?well-conceptualizedwell-developedrelevantdirect and clearfocusedincludes all components
  • sleep walking OR sleepwalking OR Sleep Walking Disorderscauses OR reasonschildren OR kids
  • 5. Display your citations  Other options include:Summary (one line); Abstract (citation, abstract, and MeSH headings)MEDLINE (text format which includes field tags, used for importing into bibliographic management software like Reference Manager, RefWorks, or EndNote)Limits Part III B Searching in specific fieldsSelect limits that restrict your search results. Click on Limits above the PubMed query box to refine the search strategy to incorporate the language and year range. Your retrieval will still include all the PubMed in process records.  IMPORTANT - If you add limits for any of the following: age group, publication type, human or animal, gender or subset you will eliminate retrieval of the PubMed in process records that are waiting for full MEDLINE indexing. Remember, the LIMITS you choose stay in effect for every search until you turn them off.2. Talk about the Boolean operators and make sure participants are comfortable with Boolean operators and stress need for operators to be in UPPER CASE Good example of need for upper case operatorsInfection and immunity VERSUS infection AND immunityThe first search yields all hits from the journal Infection and Immunity whereas the other maps to MESH terms and ‘text word’ searches as expected.
  • Pubget - based on PubMed/MEDLINE but gets to the PDF right away, provided the journal is available for free or the subscription is being paid for
  • LigerCat- is a search tool for PubMed that displays tag clouds of key words (MeSH descriptors) associated with the result set. Also, it facilitates the use of plain language queries or molecular sequences to search the PubMed database for articles or to search for journal titles.LigerCat also serves a Publication Data Histogram.
  • PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.PubMed Central Canada is a free digital archive of full-text, peer-reviewed health and life sciences literature based on PubMed Central, the archive developed by the US National Library of Medicine. The search interface allows anyone to browse, search and download articles. PMC Canada is a partnership between the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), the Canadian Institutes of Health Research (CIHR), and the US National Library of Medicine (NLM).
  • GoPubMed- searching PubMed/MEDLINE with Gene Ontology and MeSHGoPubMed = search for breast cancer to show journal and Mesh Then search for cell to show gene ontology too
  • Quertle - a free, semantic-based search engine for PubMed, full-text articles, NIH Grants, TOXLINE, and news
  • Introduction to PubMed for LIS students

    1. 1. Introduction to PubMed for LIS Students<br />Nazi Torabi<br />Research & Instructional Librarian <br />Allyn & Betty Taylor Library<br />March 30, 2011<br />http://www.slideshare.net/ntorabi/<br />
    2. 2. What PubMed is<br />MeSH (Medical Subject Headings)<br />Searching PubMed<br />MyNCBI<br />Alternative interfaces<br />
    3. 3.
    4. 4. PubMed<br />
    5. 5. What is PubMed?<br /><ul><li>Database of biomedical journal citations and abstracts
    6. 6. US National Library of Medicine (NLM)
    7. 7. Freely accessible online
    8. 8. Over 20 Million Citations
    9. 9. Date coverage back to 1950</li></li></ul><li>What Makes up PubMed?<br /><ul><li>PubMed ‑ indexed for MEDLINE
    10. 10. PubMed ‑ as supplied by publisher
    11. 11. PubMed ‑ in process
    12. 12. PubMed
    13. 13. PubMed – OLDMEDLINE</li></li></ul><li>PubMed vs. MEDLINE<br /><ul><li>PubMed ‑ indexed for MEDLINE
    14. 14. PubMed ‑ as supplied by publisher
    15. 15. PubMed ‑ in process
    16. 16. PubMed
    17. 17. PubMed – OLDMEDLINE</li></li></ul><li>MeSH<br />
    18. 18. Keyword Versus Subject Searching<br />Keyword<br />MeSH<br />Adrenaline<br />Epifrin<br />Epinephrine<br />Epitrate<br />Lyophrin<br />Micronefrin<br />Racepinephrine……..<br />Epinephrine<br />
    19. 19. MeSH<br />Includes five types of terms <br /><ul><li>Headings
    20. 20. Subheadings
    21. 21. Supplementary Concept Records (chemical and substances)
    22. 22. Publication Types
    23. 23. Grant Support </li></li></ul><li>Main Branches <br />All MeSH Categories<br /><ul><li>Anatomy Category +
    24. 24. Organisms Category +
    25. 25. Diseases Category +
    26. 26. Chemicals and Drugs Category +
    27. 27. Analytical, Diagnostic and Therapeutic Techniques and Equipment Category +
    28. 28. Psychiatry and Psychology Category +
    29. 29. Phenomena and Processes Category +
    30. 30. Disciplines and Occupations Category +
    31. 31. Anthropology, Education, Sociology and Social Phenomena Category +
    32. 32. Technology and Food and Beverages Category +
    33. 33. Humanities Category +
    34. 34. Information Science Category +
    35. 35. Persons Category +
    36. 36. Health Care Category +
    37. 37. Pharmacological Actions Category +
    38. 38. Publication Type Category +
    39. 39. Check Tags Category +
    40. 40. Subheadings Category +
    41. 41. Geographical Locations Category +</li></li></ul><li>Searching PubMed<br />
    42. 42. Sample Search Question <br /> What are the causes of sleep walking in children? <br />
    43. 43. A Structured Search Methodology<br />1. Identify the search question (PICOTT)<br />2. Isolate the main concepts<br />3. Search each concept separately<br />4. Combine search sets<br />5. Evaluate results and modify strategy<br />6. Apply limits (if needed)<br />
    44. 44. What are the causes of sleep walking in children? <br /><ul><li> sleep walking
    45. 45. causes
    46. 46. children</li></li></ul><li>PubMed<br />
    47. 47. Sample Search Question <br /> What is the diagnostic utility of the urine biological tumor marker nmp22 (nuclear matrix protein 22) in detecting recurrence of bladder cancer?<br />Adapted from http://ebmlibrarian.wetpaint.com/page/Oncology/links<br />
    48. 48. Research Question<br /><ul><li>Patient or Population
    49. 49. Intervention; Prognostic Factor; Exposure
    50. 50. Comparison
    51. 51. Outcome
    52. 52. Type of Question
    53. 53. Type of Study</li></li></ul><li>What is the diagnostic utility of the urine biological tumor marker nmp22 (nuclear matrix protein 22) in detecting recurrence of bladder cancer? <br /><ul><li>P bladder cancer patients
    54. 54. I nmp -22
    55. 55. C
    56. 56. O cancer recurrence
    57. 57. T diagnosis
    58. 58. T comparison to gold standard</li></li></ul><li>PubMed<br />
    59. 59. MyNCBI<br />
    60. 60. My NCBI<br /><ul><li>Customize PubMed display
    61. 61. Save collections
    62. 62. Save search strategies
    63. 63. Set up alerts
    64. 64. Need to register for My NCBI or sign in via Partner Organization</li></li></ul><li>Alternative interfaces<br /><ul><li>Pubget
    65. 65. LigerCat
    66. 66. PubMed Central
    67. 67. GoPubMed
    68. 68. Quertle</li></li></ul><li>Pubget<br />
    69. 69. LigerCat<br />
    70. 70. PubMed Central (PMC)<br /><ul><li>PMC
    71. 71. PMC Canada </li></li></ul><li>GoPubMed<br />
    72. 72. Quertle<br />
    73. 73. PubMedOnline Training<br />Quick animated Tutorials <br />http://www.nlm.nih.gov/bsd/disted/pubmed.html#qt<br />More Tutorials <br />http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/<br />Tutorials on MeSH<br />http://www.nlm.nih.gov/bsd/disted/video/<br />
    74. 74. Associate Fellowship Program though NLM<br /> Each year NLM offers up to eight one-year postgraduate training fellowships to recent graduates of an ALA-accredited library school. Fellows spend a year at NLM training for future leadership positions in medical librarianship. Associate Fellows are offered an optional second year at another health sciences library or information center. For an application and details see the Program web page: http://www.nlm.nih.gov/about/training/associate/index.html<br />
    75. 75. What PubMed is<br />MeSH (Medical Subject Headings)<br />Searching PubMed<br />MyNCBI<br />Alternative interfaces<br />
    76. 76. Questions<br />Need library related assistance?Please don’t hesitate to contact us:<br />Nazi Torabi<br />519-661-2111 x88992 <br />ntorabi@uwo.ca <br />IM a librarian<br />https://www.lib.uwo.ca/chat/<br />

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