Lesson 2:Internet Tool in life Sciences Research

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Lesson 2:Internet Tool in life Sciences Research

  1. 1. 2Internet Tool in life Sciences Research D.ALQahtani
  2. 2. Lessons 1- Essentials 2- Searching 3- Using MeSH 4- Working with Results 5- Jeopardy game D.ALQahtani
  3. 3. 2- Searching D.ALQahtani
  4. 4. 2- SearchingSearching PubMed is it Similar toSearching the Internet? Example: A Google phrase search for: recent harvard faculty publications , click HERE Click HERE to see the same search pasted into PubMed Click HERE to see a well designed PubMed search on the same topic D.ALQahtani
  5. 5. 2- SearchingDoes Google Search PubMed? Yes - Google and Google Scholar both search some of the contents of PubMed, so we will find PubMed citations in our Google results D.ALQahtani
  6. 6. 2- Searching BE aware that Google Scholar is up to several months behind PubMed and does not search PubMed in its entirety D.ALQahtani
  7. 7. 2- Searching Do you want to see what is the difference ? A Google Scholar Search Retrieves only aboutlimited to PubMed citations from 2008 119,000 results Retrieves over 800,000 A PubMed Search for 2008 articles results D.ALQahtani
  8. 8. 2- SearchingBottom Line 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 D.ALQahtani
  9. 9. 2- SearchingHow a Keyword Search Works in PubMed ? 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. PubMed does NOT search the full text of the article D.ALQahtani
  10. 10. 2- SearchingTry a Keyword Search in PubMed: Click in the query box. Type oral cancer and click Enter or Go. The first 20 references matching your search will appear. Near the top look for "Items 1 to 20 of X." X indicates the total number of search results D.ALQahtani
  11. 11. 2- SearchingTo view automatic term mapping in action 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 (To include all variations of the word. Ex: mouth , neoplasms, etc.). It makes your job easier! http://www.ncbi.nlm.nih.gov/pubmed?term=oral%20 cancer D.ALQahtani
  12. 12. 2- SearchingCombining Search Terms Quotes “ “ are rarely necessary in PubMed: Click Clear to remove the previous search. Then type “oral cancer" in the search box, this time surrounded by quotation marks. Click Go and then click Details to see what happens. Using quotes turns off the automatic term mapping. You are now only searching for the phrase oral cancer, and not the MeSH term mouth neoplasm or synonyms. http://www.ncbi.nlm.nih.gov/pubmed?term=%22oral %20cancer%22 In PubMed, use quotes only if you are having trouble finding an exact phrase D.ALQahtani
  13. 13. 2- SearchingTo add terms to your search you canuse AND, OR or NOT, which should be capitalized to ensure best results D.ALQahtani
  14. 14. 2- SearchingExamples Oral AND cancer Using AND will retrieve fewer results because both terms must be present in the reference Oral OR cancer Using OR will retrieve more results because either term can be present in the reference. Oral not cancer Use NOT to exclude a search term from your search. Use NOT with caution because it may eliminate relevant results. D.ALQahtani
  15. 15. D.ALQahtani
  16. 16. 2- Searching Note D.ALQahtani
  17. 17. 2- SearchingUse Parentheses ( ) For Longer Searches PubMed processes ANDs, ORs & NOTs in a left-to-right sequence D.ALQahtani
  18. 18. 2- SearchingUse Parentheses ( ) For Longer Searches  Click Clear to clear the query box.  You want to research treatment of oral cancer .  Type in: oral cancer AND chemotherapy OR radiotherapy .  Click GO These results are NOT on-target because PubMed retrieved all occurrences of “radiotherapy" in the database. The hits containing radiotherapy will not necessarily contain oral cancer. D.ALQahtani
  19. 19. 2- SearchingUse Parentheses ( ) For Longer Searches Using parentheses would change the Example order in which PubMed processes oral cancer AND the search statement (chemotherapy OR radiotherapy) D.ALQahtani
  20. 20. 2- SearchingPubMed Advanced Search Builder Allows you to set parameters for your search, which may result in a more relevant retrieval http://www.ncbi.nlm.nih.gov/pubmed/a dvanced D.ALQahtani
  21. 21. 2- Searching Filters Narrow Your Search D.ALQahtani
  22. 22. 2- SearchingAuthor Search There are ways to do this in PubMed D.ALQahtani
  23. 23. 2- Searching Author Search1. Limit by Author Name: Click the advanced search and thenSearch by Author. It will suggest names for you as you type. You canalso click Add Another Author http://www.ncbi.nlm.nih.gov/pubmed/a dvanced D.ALQahtani
  24. 24. 2- Searching Author Search2. Or, Type Directly in the Search Box: Enter the last name, aspace, then first and middle initial (if known), with no punctuation Example D.ALQahtani
  25. 25. 2- Searching Author Search3. Single citation matcher Example D.ALQahtani
  26. 26. 2- Searching Citation SearchThere are several ways to find specific citations or groupsof citations in PubMed: 1. PubMeds Citation Sensor will 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) D.ALQahtani
  27. 27. Citation sensor found 1 article D.ALQahtani
  28. 28. 2- Searching Citation Search2. The Single Citation Matcher allows you to searchspecific fields (like Author or Title) and returns citationsthat match those criteria. Single Citation Matcher isavailable from the blue sidebar on the PubMed homepage. D.ALQahtani
  29. 29. http://www.ncbi.nlm.nih.gov/pubmed/citmatch D.ALQahtani
  30. 30. 2- SearchingScenario Your supervisor asks you to read the articles written by Dr. Zhuang that were published in the journal Journal of oral pathology & medicine What will you DO D.ALQahtani
  31. 31. 1 2 3 4 D.ALQahtani
  32. 32. D.ALQahtani
  33. 33. 2- Searching Citation Search3. Field Searching allows you to specify exactly what tosearch using A- By Tags B- Using advanced search D.ALQahtani
  34. 34. 2- SearchingCitation SearchA- By Tags Field Name Tag Search ResultsAuthor Name [au] Smith jd[au] Articles authored by jd smith Examplehttp://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&term=smith%20jd% 5bau%5d D.ALQahtani
  35. 35. 2- SearchingCitation SearchA- By Tags Field Name Tag Search ResultsInstitutional Articles authored by persons [affl] harvard[affl]Affiliation affiliated with Harvard school Examplehttp://www.ncbi.nlm.nih.gov/pubmed?term=King%20saud%20university%5BAffiliation% 5D D.ALQahtani
  36. 36. 2- SearchingCitation SearchA- By Tags Field Name Tag Search Results [jour] jama[jour] Articles published in JAMAJournal Title Examplehttp://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&term=jama%5bjour %5d D.ALQahtani
  37. 37. 2- SearchingCitation SearchA- By Tags Field Name Tag Search ResultsTitle Words [ti] cancer[ti] Articles with cancer in the title Examplehttp://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&term=cancer%5bti% 5d D.ALQahtani
  38. 38. 2- SearchingScenario Again , Your supervisor asks you to read the articles written by Dr. Blood that were also published in the journal Blood . What will you DO this time ? D.ALQahtani
  39. 39. 2- Searching1- Click Clear to clear your previous search and Uncheckthe Limits box to remove any left over Limits2- In the query box, type blood AND blood, then click GO Oops ! 3 million search results! D.ALQahtani
  40. 40. 2- SearchingSO , Force PubMed to search in a specific field Type the following in the query box: blood[au] AND blood[jour] (AND must be capitalized here) Enter field tags in square brackets [] immediately following the terms. Click Go super, only 7 articles D.ALQahtani
  41. 41. 2- SearchingCitation Search B- Using advanced search D.ALQahtani
  42. 42. 123 4 The same thing , 7 articles D.ALQahtani
  43. 43. 2- Searching Heres a Quick Summary of "Searching" When you enter a keyword in the query box, PubMed will1 search for that word and its synonyms in all the fields (author, abstract, title etc.) used to describe an article2 The Details tab allows you to see if PubMed has mapped your search correctly3 Use AND, OR, NOT and/or parentheses to create longer search statements D.ALQahtani
  44. 44. 2- Searching Heres a Quick Summary of "Searching" Selecting filters places parameters on your search4 (date, journal title, study type etc.). Search by author using this format: smith bj. Or, select5 advanced search, and then Add Author Type partial citations utilizing citation sensor into the6 PubMed search box, or use the Single Citation Matcher7 Search with field tags or advanced search tab to limit your search to a specific field (author, title, etc) D.ALQahtani
  45. 45. Reference1- Gustave L. and Janet W. Levy Library of Mount Sinai School of Medicine D.ALQahtani
  46. 46. End of the lessonTHANK YOU 2 D.ALQahtani

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