Lesson 2#Scientific Research Skills

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Lesson 2#Scientific Research Skills

  1. 1. Scientific Research Skills<br />Scientific Research Skills - D.ALQahtani<br />2<br />
  2. 2. Lessons<br />Scientific Research Skills - D.ALQahtani<br />1- Essentials <br />2- Searching<br />3- Using MeSH<br />4- Working with Results<br />5- Referencing <br />
  3. 3. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />
  4. 4. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Searching PubMed is it Similar to Searching the Internet?Example: <br />A Google phrase search for: recent harvard faculty publications , click HERE<br />Click HERE to see the same search pasted into PubMed<br />Click HERE to see a well designed PubMed search on the same topic<br />
  5. 5. Yes - Google and Google Scholar both search someof the contents of PubMed, so we will find PubMed citations in our Google results<br />Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Does Google Search PubMed?<br />
  6. 6. BE aware that Google Scholar is up to several months behind PubMed and does not search PubMed in its entirety<br />Scientific Research Skills - D.ALQahtani<br />2- Searching<br />
  7. 7. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Do you want to see what is the difference ? <br />A Google Scholar Searchlimited to PubMed citations from 2008<br />Retrieves only about 119,000 results<br />A PubMed Search for 2008 articles<br />Retrieves over 800,000 results<br />
  8. 8. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Bottom Line<br />Google and Google Scholar can be a quick and easy way to get started on a search. However, they do not comprehensively search the peer-reviewed biomedical literature. PubMed does<br />
  9. 9. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />How a Keyword Search Works in PubMed ?<br />When you enter a keyword into the query box, PubMed will search for that word and its synonyms, in all the fields (author, journal title, title word, MeSH heading, abstract, publication date etc.) used to describe an article.<br />PubMed does NOT search the full text of the article<br />
  10. 10. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Try a Keyword Search in PubMed:<br />Click in the query box. Type oral cancer and click Enter orGo.The first 20 references matching your search will appear. Near the top look for &quot;Items 1 to 20 of X.&quot; X indicates the total number of search results<br />
  11. 11. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />To view automatic term mapping in action<br /> Click on the Details button. You will see how PubMed has automatically translated your search to include the synonym for oral cancer. And, it is automatically searching the term as a MeSH term<br />(To include all variations of the word. Ex: mouth , neoplasms, etc.). It makes your job easier!<br />
  12. 12. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Combining Search Terms<br />Quotes“ “ are rarely necessary in PubMed: Click Clear to remove the previous search. Then type “oral cancer&quot; in the search box, this time surrounded by quotation marks. Click Go and then click Details to see what happens. Using quotes turns offthe automatic term mapping. You are now only searching for the phrase oral cancer, and not the MeSH term mouth neoplasm or synonyms. <br />In PubMed, use quotes only if you are having trouble finding an exact phrase<br />
  13. 13. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />To add terms to your search you can use AND, OR or NOT, which should be capitalized to ensure best results<br />
  14. 14. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Examples<br />
  15. 15. Scientific Research Skills - D.ALQahtani<br />
  16. 16. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />PubMed automatically puts an AND between two concepts.<br /> So, oral cancer retrieves the same number of results as oral AND cancer<br />Note<br />
  17. 17. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Use Parentheses( ) For Longer Searches<br />PubMed processes ANDs, ORs & NOTs in a left-to-right sequence<br />
  18. 18. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Use Parentheses ( ) For Longer Searches<br /><ul><li>Click Clear to clear the query box.
  19. 19. You want to research treatment of oral cancer .
  20. 20. Type in:oral cancer AND chemotherapy OR radiotherapy .
  21. 21. Click GO</li></ul>These results are NOT on-target because PubMed retrieved all occurrences of “radiotherapy&quot; in the database. The hits containing radiotherapy will not necessarily contain oral cancer.<br />
  22. 22. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Use Parentheses ( ) For Longer Searches<br />Using parentheses would change the order in which PubMed processes the search statement <br />Example<br />oral cancer AND (chemotherapy OR radiotherapy)<br />
  23. 23. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Limits<br />The Limits Tab allows you to set parameters for your search, which may result in a more relevant retrieval<br />Helpful limits include author, journal, date, publication type (review article, randomized controlled trial etc.), language, human or animal study, age, and gender. <br />
  24. 24. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Limits<br /><ul><li> Click Clear to clear your previous search.
  25. 25. Then, once again type oral AND cancer (or oral cancer ) in the query box and click GO.
  26. 26. Adding another concept makes the number of results smaller, but there are still too many articles.
  27. 27. Click Limits to narrow the search.
  28. 28. Select the Following Limits: Dates-Published in the Last 5 years;Languages- English; Type of Article- Review; Ages- Middle Aged, 45-64 years. Then, click Go.</li></li></ul><li>Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Limits Narrow Your Search<br />You should have retrieved approximately 239 articles - much smaller and more manageable than the 84986 retrieved without using Limits<br />
  29. 29. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Author Search<br />Finding an author&apos;s publications is one of the most common reasons for using PubMed<br />There are 3 ways to do this in PubMed<br />
  30. 30. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Author Search<br />1.Limit by Author Name: Click theLimitsTaband then Search by Author. It will suggest names for you as you type. You can also click Add Another Author<br />
  31. 31. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Author Search<br />2.Or,Type Directly in the Search Box: Enter the last name, a space, then first and middle initial (if known), with no punctuation<br />Example<br />http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&orig_db=PubMed&term=smith%20bj<br />
  32. 32. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Author Search<br />3.Full Author Names may be searched for citations published in 2002 or later, if the full author name is mentioned in the article. Ex. brian j smith<br />Example<br />http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&orig_db=PubMed&term=Brian%20J%20Smith<br />
  33. 33. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />There are several ways to find specific citations or groups of citations in PubMed:<br />1. PubMed&apos;sCitation Sensorwill automatically detect most citations typed into the search box. Type in part of the citation, or as much as you know (Example: katayama cell 2006)<br />
  34. 34. Scientific Research Skills - D.ALQahtani<br />Citation sensor found 1 article <br />
  35. 35. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />2. The Single Citation Matcherallows you to search specific fields (like Author or Title) and returns citations that match those criteria. Single Citation Matcher is available from the blue sidebar on the PubMed homepage. <br />
  36. 36. Scientific Research Skills - D.ALQahtani<br />
  37. 37. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Scenario<br />Your supervisor asks you to read the articles written by Dr. Zhuangthat were published in the journal Journal of oral pathology & medicine<br />What will you DO<br />
  38. 38. Scientific Research Skills - D.ALQahtani<br />1<br />2<br />3<br />4<br />
  39. 39. Scientific Research Skills - D.ALQahtani<br />
  40. 40. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />3. Field Searchingallows you to specify exactly what to search using<br />A- By Tags<br />B- Using advanced search <br />
  41. 41. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />A- By Tags<br />
  42. 42. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />A- By Tags<br />
  43. 43. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />A- By Tags<br />
  44. 44. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />A- By Tags<br />
  45. 45. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Scenario<br />Again , Your supervisor asks you to read the articles written by Dr. Blood that were also published in the journal Blood .<br />What will you DO this time ?<br />
  46. 46. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />1- Click Clear to clear your previous search and Uncheck the Limits box to remove any left over Limits<br />2- In the query box, type blood AND blood, then click GO<br />Oops ! 3 million search results! <br />
  47. 47. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />SO , Force PubMed to search in a specific field<br />Type the following in the query box: <br />blood[au] AND blood[jour]<br />(AND must be capitalized here)<br />Enter field tags in square brackets [] immediately following the terms. Click Go<br />super, only 7 articles <br />
  48. 48. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Citation Search<br />B- Using advanced search <br />
  49. 49. Scientific Research Skills - D.ALQahtani<br />1<br />2<br />3<br />4<br />The same thing , 7 articles <br />
  50. 50. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Here&apos;s a Quick Summary of &quot;Searching&quot;<br />When you enter a keyword in the query box, PubMed will search for that word and its synonyms in all the fields (author, abstract, title etc.) used to describe an article<br />1<br />The Details taballows you to see if PubMed has mapped your search correctly<br />2<br />Use AND, OR, NOT and/or parentheses to create longer search statements <br />3<br />
  51. 51. Scientific Research Skills - D.ALQahtani<br />2- Searching<br />Here&apos;s a Quick Summary of &quot;Searching&quot;<br />Selecting Limits places parameters on your search (date, journal title, study type etc.).<br />4<br />Search by author using this format: smith bj. Or, select Limits, and then Add Author<br />5<br />Type partial citations utilizing citation sensor into the PubMed search box, or use the Single Citation Matcher<br />6<br />7<br />Search with fieldtags or advanced search tab to limit your search to a specific field (author, title, etc)<br />
  52. 52. Scientific Research Skills - D.ALQahtani<br />Reference<br />1- Gustave L. and Janet W. Levy Library of Mount Sinai School of Medicine<br />
  53. 53. Thank you<br />End of the lesson<br />Scientific Research Skills - D.ALQahtani<br />2<br />

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