1. Copyright OpenHelix. No use or reproduction without express written consent1

2. NCBI PubMed NCBI PubMed: Finding the Literature You Need Materials prepared by: Cynthia Perreault-Micale, Ph.D. Jennifer Williams, Ph.D. www.openhelix.com Updated: Q2 2012

3. Copyright OpenHelix. No use or reproduction without express written consent3 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

4. Copyright OpenHelix. No use or reproduction without express written consent4 PubMed Overview  contains millions of abstracts from thousands of journals  covers diverse topics within the biomedical field  citations come mostly from MEDLINE  allows efficient searching of the biomedical literature  is linked to many other databases http://www.pubmed.gov

5. Copyright OpenHelix. No use or reproduction without express written consent5 PubMed Homepage: Features Help Search Function Tools Additional Links My NCBI http://www.pubmed.gov Help More Resources

6. Copyright OpenHelix. No use or reproduction without express written consent PubMed Homepage: More Features & Help 6 Help NCBI Help http://www.pubmed.gov Other NCBI Resources

7. Copyright OpenHelix. No use or reproduction without express written consent7 PubMed: Reference and Citation http://nar.oxfordjournals.org/content/40/D1/D13

8. Copyright OpenHelix. No use or reproduction without express written consent8 PubMed: Member of Entrez Interlinked Network Over 40 molecular and literature databases in Entrez system Enter Search term Click http://www.ncbi.nlm.nih.gov/sites/gquery

9. Copyright OpenHelix. No use or reproduction without express written consent9 Global Query: Results in All Databases PubMed Results across all Entrez databases Click ? for database description One query Click database, icon, or # of results to view

10. Copyright OpenHelix. No use or reproduction without express written consent10 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

11. Copyright OpenHelix. No use or reproduction without express written consent11 Beginning a Basic Search: NCBI Homepage http://www.ncbi.nlm.nih.gov/ Enter search term & then click Search OR click Search to go to PubMed’s homepage PubMed

12. Copyright OpenHelix. No use or reproduction without express written consent12 http://www.pubmed.gov Beginning a Basic Search: PubMed Homepage  Our search example will be nerve regeneration auto-complete menu takes you to results Turn off Enter Search term

13. matches Basic Search: Results header 13Copyright OpenHelix. No use or reproduction without express written consent # of Results Display Settings Click here

14. Copyright OpenHelix. No use or reproduction without express written consent14 Formatting Options Basic information - authors, title, journal, citation status Summary Format

15. Copyright OpenHelix. No use or reproduction without express written consent15 More Formatting Options Summary (text) Abstract PMID List Abstract (text) MEDLINE XML

16. Copyright OpenHelix. No use or reproduction without express written consent16 Outputting Results Also saves search in My NCBI Send to http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Exporting_citations_

17. Copyright OpenHelix. No use or reproduction without express written consent17 Results Filters All Manage Filters Filters: click to view subsets of results Review Full Text Select confirm

18. Copyright OpenHelix. No use or reproduction without express written consent18 More Information Related Titles Free full-text Find data Search details Recent activity

19. Copyright OpenHelix. No use or reproduction without express written consent19 Article Report Also MeSH Terms for older papers

20. Copyright OpenHelix. No use or reproduction without express written consent20 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

21. Advanced search click Help tip Copyright OpenHelix. No use or reproduction without express written consent21 Advanced Search Builder

22. Copyright OpenHelix. No use or reproduction without express written consent22 Advanced Search Builder, cont. count

23. Copyright OpenHelix. No use or reproduction without express written consent23 Advanced Search Builder: Edit & Results Either Build area or Edit area is active, Not both Search Builder area is now gone Manually add search criteria

24. click Copyright OpenHelix. No use or reproduction without express written consent24 Specialized Queries - MeSH MeSH terms can improve searches Not immediately available upon publication heart attack click

25. Copyright OpenHelix. No use or reproduction without express written consent25 MeSH Query Results entry terms hierarchy MeSH term subheadings Search options

26. Copyright OpenHelix. No use or reproduction without express written consent26 MeSH Query PubMed Results Search = myocardial infarction AND (diet therapy OR drug therapy OR economics) AND genetics Results = 90 hits (vs 183,000+ for “heart attack”)

27. Copyright OpenHelix. No use or reproduction without express written consent27 Journal & Single Citation Searches A tool to find a PubMed article

28. Copyright OpenHelix. No use or reproduction without express written consent28 Clinical Queries Search for “pancreatic cancer” Focused clinical results

29. Copyright OpenHelix. No use or reproduction without express written consent29 Topic-Specific Queries Queries for many topics in PubMed

30. Copyright OpenHelix. No use or reproduction without express written consent30 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

31. Copyright OpenHelix. No use or reproduction without express written consent31 (lee hk[AU] AND "Journal of Neurochemistry"[TA]) AND “nerve regeneration” Complex Boolean Search: Syntax Boolean Operators (AND, NOT, OR) Field Qualifiers: Author = [AU], Journal Title = [TA] Parenthesis  Quotes: “nerve regeneration”  Wildcard: regen* = regenerate or regeneration  No Field Qualifier = All Fields or [ALL] See Search details

32. Copyright OpenHelix. No use or reproduction without express written consent32 Complex Boolean Search: Field Qualifiers Common field qualifiers: Author = [AU] Journal Title = [TA] Title = [TI] Text Words = [TW] Qualifier Tags Field Descriptions

33. Search: (Rapoport t[AU] AND cell[TA]) AND Harvard[AD] Copyright OpenHelix. No use or reproduction without express written consent33 Complex Boolean Search: Example Edit your query here and click on Search

34. Copyright OpenHelix. No use or reproduction without express written consent34 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

35. Copyright OpenHelix. No use or reproduction without express written consent35 username My NCBI: Sign In or Register password

36. Copyright OpenHelix. No use or reproduction without express written consent36 My NCBI includes:  Search databases  My Bibliography  Recent Activity  Save Searches  Collections  Filters  Customization options My NCBI

37. Copyright OpenHelix. No use or reproduction without express written consent37 Customization Basic search http://www.ncbi.nlm.nih.gov/myncbi/manageportlets/ My Bibliography Recent Activity Collections Saved Searches Filters NCBI Search BLAST

38. Copyright OpenHelix. No use or reproduction without express written consent38 Bibliography Build bibliography from PubMed results Bibliography help: http://www.ncbi.nlm.nih.gov/books/NBK53595/

39. Copyright OpenHelix. No use or reproduction without express written consent39 Saved Searches BioSystem saved searches PubMed saved searches

40. Copyright OpenHelix. No use or reproduction without express written consent40 Collections Permanent collections, by default Created collections, Send to option Collections include:  My Bibliography  Favorites  Other Citations  User-created Collections

41. Copyright OpenHelix. No use or reproduction without express written consent41 Collections Basic PubMed Filters

42. Chemical Info Molecular DB Gender Clinical queries Books links Gene links Copyright OpenHelix. No use or reproduction without express written consent42 Filters My NCBI: Adding Power to Your NCBI & PubMed Searches bioinformatics education Counts

43. Copyright OpenHelix. No use or reproduction without express written consent43 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

44. Copyright OpenHelix. No use or reproduction without express written consent44 PubMed Homepage Services: New & Noteworthy https://www.nlm.nih.gov/pubs/techbull/jf12/jf12_pm_versioning.html For further info on versioning also see: http://www.nlm.nih.gov/services/article_versions.html

45. Copyright OpenHelix. No use or reproduction without express written consent45 PubMed Homepage Services: Batch Matcher upload PubMed or PubMed Central enter

46. Copyright OpenHelix. No use or reproduction without express written consent46 PubMed Homepage Services: E-Utilities Next slide

47. Copyright OpenHelix. No use or reproduction without express written consent47 PubMed Homepage Services: LinkOut More info Single Citations, Abstract display

48. Copyright OpenHelix. No use or reproduction without express written consent48 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

49. Copyright OpenHelix. No use or reproduction without express written consent49 PubMed Summary http://www.pubmed.gov PubMed:  contains millions of abstracts  covers diverse topics within the biomedical field  is linked to many other databases  allows basic, advanced and specialized search strategies  can be customized using My NCBI

50. Copyright OpenHelix. No use or reproduction without express written consent50 Sophisticated Search & Display Options Display Settings Output Options Basic Search Results Advanced Searches Specialized Searches Additional Information

51. Copyright OpenHelix. No use or reproduction without express written consent51 Powerful Additional Features E-Utilities For programmers My NCBI accounts Bibliography http://www.pubmed.gov

52. Copyright OpenHelix. No use or reproduction without express written consent52 PubMed Agenda Introduction and Credits Basic Search Advanced Search Options Complex Boolean Search “My NCBI” Other Features Summary Exercises PubMed : http://www.ncbi.nlm.nih.gov/pubmed/ or www.PubMed.gov

53. Copyright OpenHelix. No use or reproduction without express written consent53